ChemWiki - User contributions [en]

Mod:Hunt Research Group/solvent cavity

2019-03-13T11:20:57Z

Klw14: /* visualise in GeomVIew */

==visualise in GV6==
===option1===
[[File:Ch3ch2oh_spacefill.png|200px|thumb|right|top|space filling]]
*in the Display Format choose Molecule
*change the "Scale Radii by" and push it to maximum, ie 300%
*this is really a form of a spacefilling model
*you can also see the covalent radii by changing the "Atomic Radii" from standard to covalent

===option 2===
[[File:Ch3ch2oh_cavity.png|200px|thumb|right|top|cavity surface]]
*include "#p sp scrf(smd,solvent=water)" or what-ever your solvent is in the command line
*open the log file in GV
*choose results and "PCM solvation cavity ..."
*switch to show solid and color by atom
*move the slider to make it partially opaque

===useful information===
*turning on the print option prints some useful information
*such as the surface area and cavity volume.
<pre style="white-space: pre-wrap;">
GePol: Cavity surface area = 81.124 Ang**2
GePol: Cavity volume = 56.942 Ang**3
</pre>
==visualise in JMOL==
*to come

==visualise in GeomView==
*instructions can be found [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview| here]]

Talk:Mod:Hunt Research Group/QMMM SP Aqeuous Cu(II)

2019-01-21T12:18:23Z

Klw14: /* QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells */

== QM/MM Single Point Energy Calculation of Cu(II) and 2 Solvation Shells ==
In this example, the first solvation shell is modelled at the B3LYP 6-311G level (via Gaussian) while the second solvation shell is modelled using a classical pairwise potential (via DL_POLY). ChemShell employs an additive scheme to calculate the total QM/MM energy i.e. the total energy is the sum of the MM energy of the MM region and the QM energy of the QM region. In addition, link atoms are placed along the axis of bonds at the QM-MM boundary. More details can be found [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html here].

Create an input file called <code>energy.chm</code> with the following content:
<pre>

energy energy=e coords=cu_18water.pun \
theory= hybrid : { coupling=shift
qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22}
qm_theory=gaussian : { basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp}
mm_theory=dl_poly : mm_defs=ff.dat
}
</pre>

If you are modifying a opt.chm file generated in MolCluster, these are the only lines that are needed, so remove the other lines in the file such as "atom types", "groups", and "active atoms".

The co-ordinates of the system are read from <code>cu_18water.pun</code> (created [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) here]).
The first 22 atoms (Cu(II) + 7 waters in the first solvation shell) are modelled at the B3LYP 6-311G level.
The rest of the system is modelled using the force field defined in <code>ff.dat</code> (see [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) here] for details).
The QM and MM regions are coupled via the charge shift scheme.

The calculation should be submitted to the PBS queue to avoid overloading the login shell and inconveniencing other cx1 users (details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction here]). Don't forget to load the DL_POLY and Gaussian modules in your submit script!

The energy can be found at the end of the output (<code>energy.out</code>):
<pre>
-----------------------------------------------------------------------------------
Energy ( hybrid): -2175.199009 (a.u.)
-----------------------------------------------------------------------------------
ChemShell exiting code 0
</pre>

Talk:Mod:Hunt Research Group/VMDindexing

2018-09-12T14:12:46Z

Klw14: Created page with "When visualising things in VMD it is necessary to know that VMD starts reading the file calling the first atom, atom 0. If you use the index number from VMD and apply it to a..."

When visualising things in VMD it is necessary to know that VMD starts reading the file calling the first atom, atom 0.

If you use the index number from VMD and apply it to another file, you will be looking at a different atom, unless that file also starts from atom 0 (unlikely).

For .xyz files generated from MolClsuter or ChemShell files this means that atoms numbers in VMD are on less than in the opt.chm files.

Also when using VMD to visualise MD trajectories, this will also apply. If you want to exchange one atom for another type, changing the metal at the centre of a catalyst for example, you will need to add one to the index number from VMD to change the atom you intended to change.

Mod:Hunt Research Group

2018-09-12T14:06:33Z

Klw14: /* MD Visualisation */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advise [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to connect to HPC directory on desktop for file transfers - MacFusion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]

===Key Papers, References and Resources===
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]
#General procedure for locating transition state structures [[link]]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]

===Solvation===
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Using solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#Script to pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]
# Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]

*'''ESPs and manipulating gaussian cube files'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

===Other Visualisation===
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Installing Packmol
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
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Talk:Mod:Hunt Research Group/MolCluster

2018-09-12T13:44:34Z

Klw14: /* To visualise in VMD */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolClusterV2.3: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.
:*if you need a demo file to practice on download this history file: [[Media:TEST_CUSO4_DLPOLY_HISTORY.rtf]]

4. UPDATE - select option 1 to cut a cluster containing the QM region, active MM region and frozen MM region. We think options 2a and 2b are necessary for adding point charges

Select option 2 to cut clusters, then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
:-->[n]: Cut a cluster every "nth" step or configuration.
:-->[c]: Select a custom set of configurations i.e. you can specify exactly which configurations you want.
::*normally option n will be selected
::*once you have made the n or c selection options will relate to which clusters are to be cut, N.B: numbering starts from 1 (i.e. 1st timestep).
::* For option n you will give an integer to identify the "nth" step to cut at. Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::* The demo HISTORY file has only 5 steps, so if using this file select 2 to get 2 structures
::* For option c you will need to give the integer number of the specific step you want cut.
::*MolCluster will then tell you the the relevant coordinates have been generated

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
:-->[AN]: Atom number
:-->[AT]': Atom type
:-->[MN]': Molecule number
:-->[MT]: Molecule type
:-->[C]: Custom coordinates
::* If using the demo HISTORY file choose AT

You will then see a number of options from which you can specify the exact atom number/type.
::* If using the demo HISTORY file choose number 6 (this file has Cu-SO4+2000 waters, and O3 is the oxygen atom between Cu and S i.e. Cu-O-S

6. MolCluster will now ask for
:Available cluster construction definition:
:-->[R] Fixed radius
:-->[M] Specify number of each molecule type (i.e. the number of those molecules to include within the cluster radius)
::* If using the demo HISTORY file you want to select R
::MolCluster will then print out some information for you this will give you some idea of the number of atoms within various radii

7. In the next step, if 'R' was chosen, it will ask for the total radius (in Angstroms) of the cluster(s) to be cut, containing the QM, active MM and frozen MM regions. If 'M' was chosen it will ask for the number of each molecule (check ... will it be just for the water)
::* If using the demo HISTORY file you want to select 20 (this is a big radius so that we can have a QM region surrounded by an active MM region which is in turn surrounded with an inactive MM region)

8. Next it is possible that your chosen radius can cut through a molecule, thus MolCluster has two options for deciding which atoms to include/exclude at the boundary of the clusters being cut:

:-->[H]: Hard boundary - all atoms of a molecule must be within the cutoff radius to be included (i.e. molecules can be cut with some atoms appearing in the cluster and others not).
:-->[S]: Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the whole molecule will be included.
::* If using the demo HISTORY file you want to select S the soft option
::*If [H] is selected: With a hard boundary, the whole molecule (i.e. all of its atoms) has to be within the boundary. In other words, for any atom whose distance away from the origin is greater than the specified cluster radius, it’s associated molecule will not be included in the cluster. Since only full molecules are included, there will not be any dangling bonds under any circumstances.

9. Specify if the clusters are required to be neutral (Y/N).
:Vincent will add something here about how a cluster is neutralised (important for the ILs)
::* If using the demo HISTORY file you want to select Y option to have a neutral cluster

10. Decide on the output format, this can be for chemshell or a simple xyz:

:-->[C]: Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
:-->[X]: Generates the .xyz co-ordinates file only.
::*If [X] is selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.
::*If [C] selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation (Y/N).
::* If using the demo HISTORY file you want to select C for chemshell and Y for QM/MM

NOTE: there can be a central active QM region (C), an active MM region (SA) and a frozen MM region (SF) (Figure I)
[[File:Figure I.png]]

11. If your answer to step 10 was [C] (generate a ChemShell fragment input) and Y (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the '''QM region'''. Available options are:

:-->[S]: Spherical region (or threshold) centred about the defined origin (although not necessarily completely spherical if you have chosen a soft bondry)
:-->[M]: Choose the number of molecules closest to the origin that will be included.
:-->[A]: By an upper limit of atoms. Only whole molecules & those closest to the origin included.
:-->[C]: Custom region i.e. can select molecules individually to be in the QM region
:-->[O]: Spherical regions centred about one or more origins (for example we could choose S of SO4 as an origin and Cu as an origin and have two intersecting "regions")

::* If using the demo HISTORY file you want to select O for multiple origins. Then choose the number of origins as '2', since we want to define the regions centred about S and Cu. After choosing '2', it will list the atoms and the corresponding number, choose numbers corresponding to S and then include the desired radius. then choose Cu( by choosing the number corresponding to copper from the list) and then enter the radius. To choose the radii for each region, look at the radial distribution plot obtained for Cu-O(water) and S-O(water) from DL_POLY production run. Use the distance of the first minima as the radius.

:If [S] is selected, MolCluster will print out some information, estimating the number of atoms in the regions defined by specific radii to help you evaluate the best radius to choose. Choose a radius!
::* If using the demo HISTORY file you want to select 5.0 for the first solvation sphere around the Cu-SO4 ion-pair

:If [O] is selected ...

:Next MolCluster will ask you to specify the QM radius you want (in Angstroms)
::Note this radius must be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.

:If [C] is selected once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined .

12. Now MolCluster will ask you to select the type of '''active region''' definition from,
:-->[S] Spherical region centred about the origin
:-->[M] By number of total molcules closest to the origin
:-->[A] By an upper limit of total atoms closest to the origin
:-->[N] Specific numbers of each molecule type
::this is similar to choosing the total cluster size options, however the radius should be larger than the QM and smaller than the total cluster size!
::* If using the demo HISTORY file choose 'S'
::*Here four options are present, [S], [M], [A] and [N], but in the next step to select from these options, the programme lists only two options(S/N). This is just an error in the output to screen and you can still select the other two options. This will be fixed in the next version.

13. If [S] is selected, MolCluster will estimate the number of atoms within a set of radii and will ask you to enter the desired radius of the active region
::* If using the demo HISTORY file choose give a radius of 15.0Å for the active region

14. Next MolCluster will ask you to select a coordinate system under which the optimisation will take place. Three different co-ordinate systems are available in ChemShell for optimisation.
:-->[C]artesian (constraints not permitted)
:-->[D]elocalised internal coordinates (DLC)
:-->[H]ybrid delocalised internal coordinates (HDLC)
::Select C, D or H to define the coordinate system
::* If using the demo HISTORY file choose C the cartesian coordinates
::* we have had problems with the hybrid HDLC option so only choose this if you are an expert
::* HDLC are ...

15. Give the name of the output directory into which MolCluster should write files, followed by a base name 'cluster'
::* if using one of the in-house python scripts you must use 'cluster'
::* If using the demo HISTORY file perhaps use the directory "test1" and "cluster"

16. In the next step, we can save the bulk and cluster data objects to be generated for debug purposes by selecting 'Y'. if not required, select 'N' and MolCluster will generate the clusters.
::*Data objects:This was setup mainly so that it would be easier for Vincent to run some tests if there was something wrong with the clusters. He will have this option removed from the next version and perhaps instead have a ‘debug’ version of MolCluster.

::* If using the demo HISTORY file chose N

:MolCluster will now generate the clusters and files required
::* if you used a central radius you will see something like this
<pre>
Please give output basename (no spaces and only alphanumeric and underscore
characters allowed): cluster
--------------------------------------------------------------------------------
Do you want the bulk and cluster data objects to be generated for debug purposes
[Y/N]? N
--------------------------------------------------------------------------------
Creating directory 'test1/cluster_1'
--------------------------------------------------------------------------------
Generating 2x2x2 supercell...

Cluster 1 out of 5 generated...

ChemShell potential file test1/cluster_1/ff.dat...

...generated

--------------------------------------------------------------------------------

There are 18 molecules (54 atoms) in the QM region.

The total charge of the QM region is 0.0.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO System information written to test1/cluster_1/system_info.txt OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

--------------------------------------------------------------------------------

Creating directory 'test1/cluster_2'

--------------------------------------------------------------------------------

Generating 2x2x2 supercell...

Cluster 2 out of 5 generated...

ChemShell potential file test1/cluster_2/ff.dat...

...generated

--------------------------------------------------------------------------------

There are 19 molecules (57 atoms) in the QM region.

The total charge of the QM region is 0.0.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO System information written to test1/cluster_2/system_info.txt OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
</pre>

and once all the clusters have been generated you should see this:
<pre>
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

III All clusters generated. III

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

--------------------------------------------------------------------------------

Please report any bugs to Vincent Chen (vhc08@ic.ac.uk) or Gabriel Lau

(gvl07@ic.ac.uk). The log file can be found in 'temp/molcluster.log'.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO Log file copied to 'test1'. OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

--------------------------------------------------------------------------------

EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

EEE Exiting molcluster EEE

EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
</pre>

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

== To visualise in VMD ==

::* open the cluster_tiered.xyz file in vmd: File → New Molecule → Browse → select the file type → Load the file

[[File:Figure_IIa.png]]

::*To highlight each layer in the cluster, open graphical representation

[[File:Figure_IIb.png]]

::* To create a new representation: click on 'Create Rep', a new line will appear

[[File:Figure_IIc.png]]

::* In the 'Selected Atoms' type
'''name ".*1"''' for the 1st QM region and from the 'Drawing Method' select VDW
'''name ".*2"''' for the 2nd active MM region, from the 'Drawing Method' select CPK
'''name ".*3"''' for the 3rd frozen MM region, from the 'Drawing Method' select Lines

::* The highlighted layers are shown in Figure II.

[[File:Figure_IId.png]]

IMPORTANT In VMD atom numbering starts at 0, whereas the MolCluster and ChemShell files start with atom number 1. When visualising things in VMD all of the indexing will be 1 less than the atom number in opt.chm.

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat
*MolCluster will not generate cluster.pun, but it generates cluster_n.chm which is used to generate cluster.pun
*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell/3.5.0
chemsh.x cluster_n.chm</pre>
::'''NB''': check the connectivity in the cluster.pun
*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
*include the conn and mxexcl after the mm_theory. mxexcl depends on the QM region, please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
*the submit script, submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

----
*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

----

=Step-By-Step Example: Ionic Liquid Clusters=

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

*To find out how many molecules in the QM and active regions, we can open the file called ''molcluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

*Returning to the files in our subdirectory ''cluster_1'', we can open ''cluster.xyz'' (or ''cluster_tiered.xyz'') in VMD to visualise the cut cluster, '''Figure 18''' for our cluster 1. ''cluster_tiered.xyz'' is particularly useful, as it allows us to visualise each of the distinct regions. All of the atoms in the QM region are labelled with a 1 (active labelled with 2 and frozen labelled with 3), therefore we can choose to visualise the QM region only, '''Figure 19a'''. In '''Figure 19b''', all the regions are shown in different colours.

[[Image:full-cluster-1.png|thumb|center|800px|'''Figure 18'''. Cluster 1 visualised in VMD. ]]

[[Image:cluster_tiered-edit.png|thumb|center|800px|'''Figure 19'''. '''(a)''' QM region visualised in VMD. '''(b)''' All regions, visualised in different colours. ]]

----

=Cutting Embedded Cluster=
*Embedded clusters are generated in two steps
*First a cluster of specific radius is generated using MolCLuster and Chemshell
1. Load MolClusterV2.3: ./MolCluster.py

2. Enter the directory containing the FIELD and HISTORY files as in the previous case

3. Select option [4] to Generate ChemShell input for cutting embedded cluster

4. then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.
After this you can choose the step at which the clusters are to be cut

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then see a number of options from which you can specify the exact atom number/type.

6. Enter the radius (in Angstroms) of the embedded cluster(s) to be cut

7. Enter the projected radius (in Angstroms) of the active regions ( this can be any value < embedded cluster radius)

8. Then enter the charge margin - distance (in Angstroms) from the cluster boundary to the outer point charges [[File:Embedded2.png]]

9. enter the number of added point charges. This is calculated from the charge density; (4 * density * density + 2)

10. enter the symbol to represent point charge 'X'

11.Specify the output directory

12. The output directory will haven inputs 'embedded_cluster_n', if chosen 'n' in step 4 and an embedded_cluster_specs.obj file

13. Upload the directory to cx1 login shell

14. In each of the 'embedded_cluster_n' will contain a 'bulk_fragment.chm' having the coordinates

15. generate bulk.pun from bulk_fragment.chm by loading chemshell 'module load chemshell mpi' and 'chemsh.x bulk_fragment.chm'

16. submit the job using the submit script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt_embedded.sh link]

*In the second step, clusters with different regions (QM and MM) with point charges outside are cut using MolCluster

17. When the job is finished transfer the folder to the local machine with MolClusterV2.3

18. Load MolClusterV2.3: ./MolCluster.py

19. Enter the same directory containing the FIELD and HISTORY files as given in the first step

20. select option [5] to cut cluster and add point charges

21. MolCluster will ask for the directory containing 'embedded_cluster_specs.obj' of the embedded cluster(s) generated by ChemShell. (the folder containing ChemSehll output)

22. Now the cluster specifications will be asked for. enter 'Y' if you want to use the same radius for the regions as entered before or 'N' if want to change the radius

23.In the next step MolCluster will ask for the type of QM region you want to specify
-->[S] Spherical region centred about the origin
-->[M] By number of total molcules closest to the origin
-->[A] By an upper limit of total atoms closest to the origin
-->[N] Specific number of molecules closest to the origin of each molecule type
-->[C] Custom region
-->[O] Spherical volumes centred about one or more user-defined origins

24. Clusters will be cut at this point and saved to the folder having the 'embedded_cluster_specs.obj' file.

::* open embedded_cluster_n, it will have the opt.chm, ff. dat and embedded_cluster_n.chm

25. transfer the folder to cx1

26. load chemshell on cx1 and run

<pre>module load chemshell mpi
chemsh.x embedded_cluster_n.chm</pre>

* embedded_cluster_n.pun will be generated

27. open opt.chm and edit the first line "dl-find coords=embedded_cluster_n.pun\". Also make changes in the opt.chm as described in [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link] and run the optimization

28. The submit script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt_embedded2.sh link]

==='''OLD instructions that relate to MolCluster v1-7'''===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. First select option 2 to cut clusters, then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.
After this you can choose the step at which the clusters are to be cut

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then see a number of options from which you can specify the exact atom number/type.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

NOTE: there can be a central active QM region (C), an active MM region (SA) and a frozen MM region (SF) (Figure I), so far you have selected the maximum radius for the size of the cluster, now select the radius of the active MM smaller than this.

[[File:Figure I.png]]

11. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius, specified (in Angstroms) and must, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simply enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.). NOTE: if you are going to use the trajectory_analysis scripts later the base filename must be "cluster".

13. Unless in step 10 above you selected options '''[C'''] or '''[O]''' (in which case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' was selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' was selected in step 10, you will be asked to specify how many region centers you employed in setting up a non-spherical QM region.
You can choose the centre of the multiple regions via atom/molecule or use the current cluster origin. A table is provided to help you make this choice identifying atom numbers and molecules and their distance from the cluster origin.

----
::*To run ChemShell in Cartesian coordinate (MolCluster1.7):

::*open opt.chm and delete the lines:
coordinates=hdlc \
residues=
::* then run
module load chemshell/3.5.0
chemsh.x cluster_n.chm
*follow the same steps as in the previous case

----

Talk:Mod:Hunt Research Group/Starting MD

2018-08-17T16:50:58Z

Klw14: /* Number of molecules or volume of cell */

==Intro==
You have two choices depending on if this is a pure system or is a solute plus solvent. You can start from
a) molecules on a grid (not discussed here)
b) a random distribution of solvent molecules or a solute surrounded by a random config of solvent molecules
note: VMD has a solvent build for water only

A molecular liquid is different to a molten salt, molten salt doesn't need a 5K relaxation and should be run from a crystal structure rather than a packmol generated structure

Tolerance is used so that things don't overlap, it is set for water at about 2 or 3. For IL's 5 has been used.
If packmol is taking a long time to generate the simulation box it could be that the tolerance is too low. Try increasing the tolerance slightly (by 1) high tolerance gives a lower density box as larger spaces are used between molecules/ions.

==Number of molecules or volume of cell==
* define box/cell size based on relevant literature and/or what you want to do
* OR define the number of molecules you can potentially simulate in a realistic time
* then use density=mass/volume to predict the other quantity
* you do need to have an '''experimental density''' or a very good estimate (for the final temperature) in g/cm3
* see this equation '''Volume=molar mass/(0.6022*(density/number of molecules))'''
** 0.6022 is used as it combines Avagadros constant and a conversion from Å^3 to cm^3
* if you have different molecules e.g. NaCl in water, take volume of NaCl and add to the volume of water
* take the cubed root of the volume to get a first estimate of the box length
* then use packmol

==Using packmol==

Packmol webiste [http://www.ime.unicamp.br/~martinez/packmol/home.shtml]

This should all be done on a local machine, not the HPC

* first you need to build an input file, this must have the name 'file.inp'
<pre>#
# Generation of the NaCl in water
#
tolerance 2.0
filetype xyz
output nacl_1330-spce.xyz

structure na.xyz
number 1
inside box 0. 0. 0. 10. 10. 10.
end structure

structure cl.xyz
number 1
inside box -10. -10. -10. 0. 0. 0.
end structure

structure spce.xyz
number 1330
inside box -17. -17. -17. 17. 17. 17.
end structure
</pre>
* tolerance is the distance between molecules, smaller for small molecules ≈2 Å for water
* a good number for ILs is between 3.4-3.8
* filetype can be xyz or pdb (default)
* output filename i.e. the filename of the output file
* then define the individual molecules/ions to be included inside structure and end structure strings
* first define the file in which the structure coordinates are to be found (see below)
* then the number of molecules of this type in the cell
* then were to place these molecules within that cell
* this file has the format: number of atoms, descriptive title, atom identifier and xyz coordinates
<pre>
1
na
NA 0.000000 0.000000 0.000000
</pre>
* in this case we are building a cell of length approx 34Å
* it is important to make sure the 0,0,0 is in the centre, hence the -17 to +17
* we also want our Na+ and Cl- well separated, to ensure this we make sure it is distributed roughly in opposite corners of the box, but not right on the edges as we don't want the ions on the cell boundaries
* see the manual for various ways of controlling how the ions are distributed within the cell

* then run packmol by typing /directory_path/packmol < file.inp
* the resulting coordinates will be in the output file you specified
* you then want to visualise the structure in VMD to check that it looks ok

==Quick relaxation==
1. resize your box slightly
:packmol sometimes places molecule over the edges so increase the box side length by 10-20%
::so for our example (0.2*34)+34 is 40.8, rounding this down to a nice number gives a box size of 40Å
::this of courses lowers the density, which will be corrected for when you run the NPT

2. use this script to convert the output of packmol into a dlpoly readable file [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/conv_xyz2conf conv_xyz2conf.pl]
:dlpoly is highly format driven so check the dlpoly manual for the exact details
:essentially each atom is now numbered with the xyz coordinates on the following line
:notice that in the script specific atomic labels are searched and printed so if you have a different molecule you will need to edit the script to put in the new atom types you need.
:input is the filename you wish to convert excluding the .xyz extension
:for example conv_xyz2conf nacl_1330-spce
:: so nacl_1330_spce.xyz looks like this
<pre>
3992
Built with Packmol
NA 0.001779 9.402974 9.416280
CL -9.999671 -0.580455 -0.000345
OH2 -1.549154 16.628984 6.058143
HO -1.166292 16.884755 6.945835
HO -0.975087 16.999934 5.328183
OH2 -3.418933 0.347746 -2.288811
HO -3.805476 1.262661 -2.172555
HO -3.388480 0.119970 -3.262048
OH2 -15.941200 6.736377 16.160857
</pre>
:this will produce a file with the same name but extension .cfg
::and you will get something that looks like this
<pre>
Converted from Packmol XYZ
0 0 0 0.000000
0.000000000000 0.000000000000 0.000000000000 #Note: You are required to fill in the correct numbers here!
0.000000000000 0.000000000000 0.000000000000 #Note: Do not change the spacing!!!!
0.000000000000 0.000000000000 0.000000000000
NA 1
0.001779 9.402974 9.416280
CL 2
-9.999671 -0.580455 -0.000345
OH2 3
-1.549154 16.628984 6.058143
HO 4
-1.166292 16.884755 6.945835
HO 5
-0.975087 16.999934 5.328183
OH2 6
-3.418933 0.347746 -2.288811
HO 7
-3.805476 1.262661 -2.172555
HO 8
-3.388480 0.119970 -3.262048
OH2 9
-15.941200 6.736377 16.160857
</pre>
:this file needs to be copied to the CONFIG file and appropriately edited

The 0.0000 section is to do with the size of the simulation box. So whatever your box size was in packmol increase it by 10% and use this new value. Put the new box size length one in each column and one in each row (diagonal top left to bottom right).
The 0 under from in the above example should be changed to 1. The 0 under packman needs to be changed to the number of molecules in the simulation.

;now goto step 2 below

*(this is ruth's old instructions)now start a dlpoly job (skip this)
step 1. start with a box 1/2 dimensions in all directions, and equilibrate, then make \"supercell\" of 8 boxes for final equilibration and collection of data
::options for cutoff -use 10-12Å (I have used 14 Å.)
:::remember you can only get a g(r) upto cut-off
:::play with this, too large (has to recalculate lots) and you too small (??) calculation runs slower
::options for ewald -use 10-5/10-6 (I have used 10-6.)
::verlet neighbour list - I have used 0.75 (from Ruth).
:::-play with this, too large (has to recalculate lots) and you too small (??) calculation runs slower

step 2. carry out NVE simulation (this is essential to get a good starting point)
we have a fixed volume, and we want to relax the system to relax the individual molecules in other MD programs you would do a minimisation, however we will give it a little bit of energy to allow things to move around a bit. This step is more important for ILs which are less fluid, or for larger solvent molecules where moving a molecule costs a bit more energy. For something like water can go straight to room temperatures, but we will go through the motions so that you have experience.
:you need a CONTROL file
:here is our example
<pre>
dlpoly run
temperature 5.15
#pressure 0.001
ensemble nve
#ensemble npt hoover 0.2 0.2
integrator leapfrog
shake 1.0E-05
quaternion 1.0E-08
steps 5000
equilibration 500
scale 100
print 100
stack 100
stats 100
timestep 0.001
cutoff 16.000
delr 0.100
rvdw 15.000
ewald precision 1.0E-6
traj 1 100 0
job time 1000000.0
close time 1000.0
finish
</pre>

*for the shake algorithm use 1*10-6 if you have pdb or inaccurate geometry, if you have xyz 1*10-8 is better. The shake constrains all the H-bonds to this bond length.
*use the computational method to determine the bond distances and lengths used by the people developing the potential, for example if they use HF you use HF to generate your geometry!

:The minimisation options in DLPOLY don't work very well for ILs.
::T = 5K for 50 steps
:::use smaller timestep (e.g. 0.2fs) to make pressure tensor ~E+00
:::if use large timestep e.g. 2fs, pressure tensor ~E+06
::T=400K for 1000 steps
:::start from the above relaxed structure by copying the REVCON file into a new directory and calling it CONFIG
:::in case of [BMIM][BF4] or [BMIM][NO3], check that it ends at ~360K.
:::check that the pressure tensor is small ~E-01/-02.

Common problems
e.g. box may explode
check the potential for the correct units
are two cations next to each other - start from crystal structure
scale forces using the 'cap (forces)' keyword sets the max forces to what is in the brackets, careful this can be dangerous, run a second equilibration without the cap keyword.

Talk:Mod:Hunt Research Group/ChemShell files

2018-04-25T15:27:18Z

Klw14: /* opt.chm files */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 7 22 45 69 82 84 102 137 138 139 140 }\
qm_theory=gaussian : { nproc=7 maxcyc=200 scfconv=5 basisspec={ { 3-21g { N* C* } } { lanl2dz L* } } ecpspec={ { null { N* C* } } { lanl2dz L* } } g98_mem=35000000 charge=-1 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
use_pairlist=no \
mxexcl=300 \
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 } } } \
active_atoms = { 1 7 9 10 11 13 18 20 22 25 27 29 31 32 35 36 43 44 45 48 51 52 58 62 64 65 69 72 74 76 82 83 84 88 94 98 100 101 102 103 105 106 108 109 112 114 115 117 118 120 124 128 129 132 133 134 137 138 139 140 }\
list_option = full \
maxcycle = 300 \
dump = 1 \
result = cluster_opt.pun

</pre>

It is IMPORTANT that in the "basis spec" section the basis set for non pseudo-potential atoms goes first, followed by the information for the pseudo-potential atoms. The same applies for the "ecpspec" keyword.

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters. It is necessary to the have the parameters as '''C6''' and '''C12''' and in '''kCal'''

An example ff.dat file is shown below for an La NaCl system.

<pre>
vdw NA NA 87.5812212 14750.8882
vdw NA CL 522.364248 593182.84
vdw CL CL 3106.1365 24120183.2
vdw LA CL 1471.76193 6991022.6
vdw LA NA 284.384407 228931.111
vdw LA LA 667.42017 1856038.3
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

To generate the parameters for the ff.dat file some work needs to be completed!

I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.

To generate the C6 value needed the calculation needed is 4*E*sigma^6
To generate the C12 value needed the calculation needed is 4*E*sigma^12

These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.

To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.chm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/ChemShell files

2018-04-25T15:25:36Z

Klw14: /* opt.chm files */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 7 22 45 69 82 84 102 137 138 139 140 }\
qm_theory=gaussian : { nproc=7 maxcyc=200 scfconv=5 basisspec={ { 6-31g* { N* C* } } { lanl2dz L* } } ecpspec={ { null { N* C* } } { lanl2dz L* } } g98_mem=35000000 charge=-1 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
use_pairlist=no \
mxexcl=300 \
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 } } } \
active_atoms = { 1 7 9 10 11 13 18 20 22 25 27 29 31 32 35 36 43 44 45 48 51 52 58 62 64 65 69 72 74 76 82 83 84 88 94 98 100 101 102 103 105 106 108 109 112 114 115 117 118 120 124 128 129 132 133 134 137 138 139 140 }\
list_option = full \
maxcycle = 300 \
dump = 1 \
result = cluster_opt.pun

</pre>

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters. It is necessary to the have the parameters as '''C6''' and '''C12''' and in '''kCal'''

An example ff.dat file is shown below for an La NaCl system.

<pre>
vdw NA NA 87.5812212 14750.8882
vdw NA CL 522.364248 593182.84
vdw CL CL 3106.1365 24120183.2
vdw LA CL 1471.76193 6991022.6
vdw LA NA 284.384407 228931.111
vdw LA LA 667.42017 1856038.3
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

To generate the parameters for the ff.dat file some work needs to be completed!

I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.

To generate the C6 value needed the calculation needed is 4*E*sigma^6
To generate the C12 value needed the calculation needed is 4*E*sigma^12

These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.

To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.chm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/ChemShell files

2018-02-22T13:07:05Z

Klw14: /* ff.dat */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 63 73 75 93 125 126 127 128 }\
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=lanl2dz basisspec={ { lanl2dz * } } ecpspec={ { lanl2dz * } }
g98_mem=640000000 charge=-3 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=300\
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122 123 124 125 126 127 128 } } } \
active_atoms = { 1 2 4 5 6 7 9 14 15 17 20 22 24 26 27 29 30 31 37 38 39 40 43 46 47 48 53 56 58 59 63 65 67 69 70 73 74 75
78 79 83 85 87 89 91 92 93 94 96 97 99 100 103 105 106 107 108 110 111 113 117 118 120 121 122 125 126 127 128 }\
list_option = full \
maxcycle = 800\
restart = yes \
dump = 1 \
result = cluster_opt.pun

</pre>

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters. It is necessary to the have the parameters as '''C6''' and '''C12''' and in '''kCal'''

An example ff.dat file is shown below for an La NaCl system.

<pre>
vdw NA NA 87.5812212 14750.8882
vdw NA CL 522.364248 593182.84
vdw CL CL 3106.1365 24120183.2
vdw LA CL 1471.76193 6991022.6
vdw LA NA 284.384407 228931.111
vdw LA LA 667.42017 1856038.3
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

To generate the parameters for the ff.dat file some work needs to be completed!

I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.

To generate the C6 value needed the calculation needed is 4*E*sigma^6
To generate the C12 value needed the calculation needed is 4*E*sigma^12

These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.

To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.chm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/MolCluster

2018-02-22T13:05:15Z

Klw14: /* Using MolClusterV2.3: Basic Instructions */

===What is MolCluster?===
MolCluster is a tool (developed by Vincent and Gabriel) that can be used to cut clusters from MD trajectories and create the input files for ChemShell.

To use MolCluster, you will need:
* The latest version of MolCluster (available from Vincent).
* Python version 2.7.6, or above.
* The HISTORY file from which the clusters are to be cut, and the corresponding FIELD file. Note: these need to be in DL_POLY format. If you have used the 'restart' option in DL_POLY, the header of the HISTORY file may need to be amended. Additional transformations of the HISTORY and FIELD files, to convert atom labels into an acceptable format for MolCluster/ChemShell, may also be required (example given later).

===Using MolClusterV2.3: Basic Instructions===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.
:*if you need a demo file to practice on download this history file: [[Media:TEST_CUSO4_DLPOLY_HISTORY.rtf]]

4. UPDATE - select option 1 to cut a cluster containing the QM region, active MM region and frozen MM region. We think options 2a and 2b are necessary for adding point charges

Select option 2 to cut clusters, then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
:-->[n]: Cut a cluster every "nth" step or configuration.
:-->[c]: Select a custom set of configurations i.e. you can specify exactly which configurations you want.
::*normally option n will be selected
::*once you have made the n or c selection options will relate to which clusters are to be cut, N.B: numbering starts from 1 (i.e. 1st timestep).
::* For option n you will give an integer to identify the "nth" step to cut at. Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::* The demo HISTORY file has only 5 steps, so if using this file select 2 to get 2 structures
::* For option c you will need to give the integer number of the specific step you want cut.
::*MolCluster will then tell you the the relevant coordinates have been generated

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
:-->[AN]: Atom number
:-->[AT]': Atom type
:-->[MN]': Molecule number
:-->[MT]: Molecule type
:-->[C]: Custom coordinates
::* If using the demo HISTORY file choose AT

You will then see a number of options from which you can specify the exact atom number/type.
::* If using the demo HISTORY file choose number 6 (this file has Cu-SO4+2000 waters, and O3 is the oxygen atom between Cu and S i.e. Cu-O-S

6. MolCluster will now ask for
:Available cluster construction definition:
:-->[R] Fixed radius
:-->[M] Specify number of each molecule type (i.e. the number of those molecules to include within the cluster radius)
::* If using the demo HISTORY file you want to select R
::MolCluster will then print out some information for you this will give you some idea of the number of atoms within various radii

7. In the next step, if 'R' was chosen, it will ask for the total radius (in Angstroms) of the cluster(s) to be cut, containing the QM, active MM and frozen MM regions. If 'M' was chosen it will ask for the number of each molecule (check ... will it be just for the water)
::* If using the demo HISTORY file you want to select 20 (this is a big radius so that we can have a QM region surrounded by an active MM region which is in turn surrounded with an inactive MM region)

8. Next it is possible that your chosen radius can cut through a molecule, thus MolCluster has two options for deciding which atoms to include/exclude at the boundary of the clusters being cut:

:-->[H]: Hard boundary - all atoms of a molecule must be within the cutoff radius to be included (i.e. molecules can be cut with some atoms appearing in the cluster and others not).
:-->[S]: Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the whole molecule will be included.
::* If using the demo HISTORY file you want to select S the soft option
::*If [H] is selected: With a hard boundary, the whole molecule (i.e. all of its atoms) has to be within the boundary. In other words, for any atom whose distance away from the origin is greater than the specified cluster radius, it’s associated molecule will not be included in the cluster. Since only full molecules are included, there will not be any dangling bonds under any circumstances.

9. Specify if the clusters are required to be neutral (Y/N).
:Vincent will add something here about how a cluster is neutralised (important for the ILs)
::* If using the demo HISTORY file you want to select Y option to have a neutral cluster

10. Decide on the output format, this can be for chemshell or a simple xyz:

:-->[C]: Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
:-->[X]: Generates the .xyz co-ordinates file only.
::*If [X] is selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.
::*If [C] selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation (Y/N).
::* If using the demo HISTORY file you want to select C for chemshell and Y for QM/MM

NOTE: there can be a central active QM region (C), an active MM region (SA) and a frozen MM region (SF) (Figure I)
[[File:Figure I.png]]

11. If your answer to step 10 was [C] (generate a ChemShell fragment input) and Y (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the '''QM region'''. Available options are:

:-->[S]: Spherical region (or threshold) centred about the defined origin (although not necessarily completely spherical if you have chosen a soft bondry)
:-->[M]: Choose the number of molecules closest to the origin that will be included.
:-->[A]: By an upper limit of atoms. Only whole molecules & those closest to the origin included.
:-->[C]: Custom region i.e. can select molecules individually to be in the QM region
:-->[O]: Spherical regions centred about one or more origins (for example we could choose S of SO4 as an origin and Cu as an origin and have two intersecting "regions")

::* If using the demo HISTORY file you want to select O for multiple origins. Then choose the number of origins as '2', since we want to define the regions centred about S and Cu. After choosing '2', it will list the atoms and the corresponding number, choose numbers corresponding to S and then include the desired radius. then choose Cu( by choosing the number corresponding to copper from the list) and then enter the radius. To choose the radii for each region, look at the radial distribution plot obtained for Cu-O(water) and S-O(water) from DL_POLY production run. Use the distance of the first minima as the radius.

:If [S] is selected, MolCluster will print out some information, estimating the number of atoms in the regions defined by specific radii to help you evaluate the best radius to choose. Choose a radius!
::* If using the demo HISTORY file you want to select 5.0 for the first solvation sphere around the Cu-SO4 ion-pair

:If [O] is selected ...

:Next MolCluster will ask you to specify the QM radius you want (in Angstroms)
::Note this radius must be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.

:If [C] is selected once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined .

12. Now MolCluster will ask you to select the type of '''active region''' definition from,
:-->[S] Spherical region centred about the origin
:-->[M] By number of total molcules closest to the origin
:-->[A] By an upper limit of total atoms closest to the origin
:-->[N] Specific numbers of each molecule type
::this is similar to choosing the total cluster size options, however the radius should be larger than the QM and smaller than the total cluster size!
::* If using the demo HISTORY file choose 'S'
::*Here four options are present, [S], [M], [A] and [N], but in the next step to select from these options, the programme lists only two options(S/N). This is just an error in the output to screen and you can still select the other two options. This will be fixed in the next version.

13. If [S] is selected, MolCluster will estimate the number of atoms within a set of radii and will ask you to enter the desired radius of the active region
::* If using the demo HISTORY file choose give a radius of 15.0Å for the active region

14. Next MolCluster will ask you to select a coordinate system under which the optimisation will take place. Three different co-ordinate systems are available in ChemShell for optimisation.
:-->[C]artesian (constraints not permitted)
:-->[D]elocalised internal coordinates (DLC)
:-->[H]ybrid delocalised internal coordinates (HDLC)
::Select C, D or H to define the coordinate system
::* If using the demo HISTORY file choose C the cartesian coordinates
::* we have had problems with the hybrid HDLC option so only choose this if you are an expert
::* HDLC are ...

15. Give the name of the output directory into which MolCluster should write files, followed by a base name 'cluster'
::* if using one of the in-house python scripts you must use 'cluster'
::* If using the demo HISTORY file perhaps use the directory "test1" and "cluster"

16. In the next step, we can save the bulk and cluster data objects to be generated for debug purposes by selecting 'Y'. if not required, select 'N' and MolCluster will generate the clusters.
::*Data objects:This was setup mainly so that it would be easier for Vincent to run some tests if there was something wrong with the clusters. He will have this option removed from the next version and perhaps instead have a ‘debug’ version of MolCluster.

::* If using the demo HISTORY file chose N

:MolCluster will now generate the clusters and files required
::* if you used a central radius you will see something like this
<pre>
Please give output basename (no spaces and only alphanumeric and underscore
characters allowed): cluster
--------------------------------------------------------------------------------
Do you want the bulk and cluster data objects to be generated for debug purposes
[Y/N]? N
--------------------------------------------------------------------------------
Creating directory 'test1/cluster_1'
--------------------------------------------------------------------------------
Generating 2x2x2 supercell...

Cluster 1 out of 5 generated...

ChemShell potential file test1/cluster_1/ff.dat...

...generated

--------------------------------------------------------------------------------

There are 18 molecules (54 atoms) in the QM region.

The total charge of the QM region is 0.0.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO System information written to test1/cluster_1/system_info.txt OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

--------------------------------------------------------------------------------

Creating directory 'test1/cluster_2'

--------------------------------------------------------------------------------

Generating 2x2x2 supercell...

Cluster 2 out of 5 generated...

ChemShell potential file test1/cluster_2/ff.dat...

...generated

--------------------------------------------------------------------------------

There are 19 molecules (57 atoms) in the QM region.

The total charge of the QM region is 0.0.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO System information written to test1/cluster_2/system_info.txt OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
</pre>

and once all the clusters have been generated you should see this:
<pre>
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

III All clusters generated. III

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

--------------------------------------------------------------------------------

Please report any bugs to Vincent Chen (vhc08@ic.ac.uk) or Gabriel Lau

(gvl07@ic.ac.uk). The log file can be found in 'temp/molcluster.log'.

--------------------------------------------------------------------------------

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

OOO Log file copied to 'test1'. OOO

OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO

--------------------------------------------------------------------------------

EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

EEE Exiting molcluster EEE

EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
</pre>

===The Output Files===
* Each cluster will have its own directory within the directory named in step 12. These subdirectories will be named: '''cluster_1''', '''cluster_2'''...'''cluster_n'''.
* Within the main directory one will also find a file called '''molcluster.log''' and a file called '''bulk_system_info.txt'''.
::*'''molcluster.log''' is a record of the user responses to each of the MolCluster options (look at this if you have forgotten, for example, the cluster radius).
::*'''bulk_system_info.txt''' summarises information relating to the system before clusters are cut (e.g. number and type of molecules, total number of atoms, total system charge, atom labels within a molecule, atomic charges).

*If option '''[X]''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)

*If option '''[C]''', '''Y''' selected in step 9, each subdirectory '''cluster_n''' will contain:
::*The '''cluster_n.xyz''' coordinates file
::*'''system_info.txt''': Summary of the cluster (e.g. total number of molecules, total number of atoms, total charge)
::*The '''cluster_n.chm''' coordinates file. This will be used to create the '''cluster.pun''' ChemShell input file.
::*'''cluster_tiered.xyz''': xyz coordinates with the QM, active and frozen regions defined (all QM atoms listed as X1 (X=element symbol), active as X2 and frozen as X3). This file can be used to easily visualise the different regions in VMD.
::*'''conn.txt''' : the connectivity data needed by ChemShell
::*'''ff.dat''' : the forcefield in ChemShell format
::*'''opt.chm''': ChemShell input file. Options for the ChemShell optimisation specified here.

== To visualise in VMD ==

::* open the cluster_tiered.xyz file in vmd: File → New Molecule → Browse → select the file type → Load the file

[[File:Figure_IIa.png]]

::*To highlight each layer in the cluster, open graphical representation

[[File:Figure_IIb.png]]

::* To create a new representation: click on 'Create Rep', a new line will appear

[[File:Figure_IIc.png]]

::* In the 'Selected Atoms' type
'''name ".*1"''' for the 1st QM region and from the 'Drawing Method' select VDW
'''name ".*2"''' for the 2nd active MM region, from the 'Drawing Method' select CPK
'''name ".*3"''' for the 3rd frozen MM region, from the 'Drawing Method' select Lines

::* The highlighted layers are shown in Figure II.

[[File:Figure_IId.png]]

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat
*MolCluster will not generate cluster.pun, but it generates cluster_n.chm which is used to generate cluster.pun
*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell/3.5.0
chemsh.x cluster_n.chm</pre>
::'''NB''': check the connectivity in the cluster.pun
*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
*include the conn and mxexcl after the mm_theory. mxexcl depends on the QM region, please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
*the submit script, submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

----
*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

----

=Step-By-Step Example: Ionic Liquid Clusters=

Our example system:
* 256 ion pairs of [C4C1im][MeSO4]
* In total, the production run is 20ns in length; 4 lots of 5ns employing the "restart" keyword in DL_Poly.
* Our aim is to cut clusters from the last 5ns of the trajectory and create the input files for a ChemShell optimisation.

1). Create a directory within the main MolCluster directory and put the '''HISTORY''' and '''FIELD''' files here. Our directory will be called: '''BMIM_MESO4_EXAMPLE'''.

2). We now need to check to see if the HISTORY and FIELD files are in the correct format.

*As the ''restart'' keyword has been employed, two lines are missing from the header of the HISTORY file, '''Figure 1a''' and '''1b'''. MolCluster does not like this. Therefore, we need to add in the two lines that it is expecting to see, '''Figure 1c'''.

[[Image:MolCluster-HISTORY-header.png|frame|center|850px|'''Figure 1'''. Headers from selected HISTORY files '''(a)''' first 5ns of our simulation, without the use of the restart keyword, '''(b)''' last 5ns of our simulation with the restart keyword and '''(c)''' same HISTORY file as in (b), with missing lines added in. ]]

*The second problem we need to address is the atom labelling. The original atom labelling for [C4C1im][MeSO4], as used in the DL_Poly simulation, is shown in '''Figure 2a'''. Unfortunately, ChemShell has issues with this. To keep ChemShell happy, we have to change the atom labels in the HISTORY and FIELD files to the format ''elementsymbolnumber'' e.g. C2 rather than CR. Thankfully, this is quite easy to do using a script ('''sub_script.sh''', see below) written by Vincent. Firstly, however, we need to decide upon the new atom labelling. This is shown in '''Figure 2b''' for our example system. '''sub_script.sh''' requires that we have defined the atom label mappings in a file called '''sub_map.txt''' (also shown below for this system).

[[Image:BMIM-MESO4-numbering.png|thumb|center|850px|'''Figure 2'''. Original atom labelling (as used in DL_POLY MD simulation) shown in '''(a)''' and new atom labelling (suitable for MolCluster) shown in '''(b)'''. Within '''(b)''', atom labels that already had the correct format are in red. ]]

'''sub_script.sh''':

<pre>#!/bin/bash

while read line

do

#echo $line

s1=$(echo $line | awk '{ print $1 }')

s2=$(echo $line | awk '{ print $2 }')

echo "$s1 $s2"

gsed -i_bu2 "s|\<$s1\>|$s2|g" FIELD

gsed -i_bu2 "s|\<$s1\>|$s2|g" HISTORY

done < sub_map.txt</pre>

'''sub_map.txt''':
<pre>CR C3

NA N1

CW C4

HCR H2

HCW H3

HC H4

CT C6

OS4 O4

OC4 O5

HS4 H5

CS C5

CS4 C7</pre>

*Run '''./sub_script.sh'''
Note: this process may take a while, depending on the size of the file. Progress can be seen in the terminal (example shown in '''Figure 3'''), with each of the mappings specified in sub_map.txt considered in turn. The first few lines of the HISTORY file, before, and after, the relabelling can be seen in '''Figure 4'''.

[[Image:sub_map_mappings.png|thumb|center|800px|'''Figure 3'''. Example terminal output whilst running sub_script.sh ]]

[[Image:HISTORY-before-after.png|thumb|center|1000px|'''Figure 4'''. First few lines of the HISTORY file before '''(a)''' and after '''(b)''' the relabelling. ]]

3). Now our files are in the correct format, we can run MolCluster: '''./MolCluster.py'''

4). The first thing MolCluster does is to ask us to specify the directory containing the FIELD and HISTORY files. Our directory is called BMIM_MESO4_EXAMPLE. Once this has been specified, MolCluster will attempt to read the files and generate a summary of the system (from timestep 1 of the trajectory). This is shown in '''Figure 5''' for our system, and it can be seen that the information summarised by MolCluster is correct.

[[Image:MC-read-files-annotate.png|thumb|center|800px|'''Figure 5'''. After specifying the directory for the FIELD and HISTORY files, MolCluster summarises the bulk system information. ]]

5). MolCluster works out how many configurations in the HISTORY file (5000 in our example) and then asks us to specify the configurations we would like to cut a cluster from. In this case, we are going to select the '''[n]''' option (cut a cluster from every 'nth' configuration) and then specify n as an integer, in this case 1000 (i.e. n=1000, therefore cut a cluster every 1000th time step), '''Figure 6'''.

[[Image:MC-specify-config.png|thumb|center|800px|'''Figure 6'''. Specifying the configurations to create clusters for. ]]

6). We must now select how we would like to define the origin of the clusters to be cut. We are going to select option '''[AN]''' (atom number) and choose atom 1 to be the origin (for reference, in our case this is a C3 atom), '''Figure 7'''.

[[Image:origin-define.png|thumb|center|800px|'''Figure 7'''. Defining the cluster origin. ]]

7). An estimate of the number of atoms in regions with varying radii (with respect to our defined origin) is provided by MolCluster. We need to cut a cluster large enough to incorporate a reasonable number of ion pairs (bearing in mind that our cation alone, in all trans form, is over 9 Angstroms in width), but not so large that the calculation is unfeasible. The ideal size is still being investigated, but for now, let us specify a cluster radius of 15 Angstroms, '''Figure 8'''.

[[Image:cluster-radius-cut.png|thumb|center|900px|'''Figure 8'''. Choosing the cluster radius. ]]

8). MolCluster now asks us to tell it which boundary condition to use when cutting the clusters (essentially this is just how MolCluster will decide whether or not to include a molecule in the cluster for molecules at the boundary). We will select '''[S]''' (soft boundary) here. We are then asked to specify if the cluster needs to be neutral. Obviously this is only really applicable to charged systems (with counter ions), such as ionic liquids . We will select yes here, '''[Y]''', so that all our clusters have the same total charge, '''Figure 9'''.

[[Image:boundary-neutral.png|thumb|center|850px|'''Figure 9'''. Selecting boundary conditions. ]]

9). We now need to decide on the output file type. As the ultimate aim is to run QM/MM optimisations of our clusters, we need to select the options that will generate the ChemShell input files: '''[C]''', '''[Y]''', '''Figure 10'''.

[[Image:output-filetype.png|thumb|center|850px| ]]

10). A decision on how the QM region will be defined is now made. We are going to select '''[S]''' (spherical region). MolCluster then estimates the number of atoms in regions of varying radii with respect to our origin. Again, as with step 7, the optimum size has not yet been deduced. However, from previous tests, a QM radius of 7 Angstroms results in a manageable number of ions and is large enough to observe local structural features. Therefore, we shall specify a radius of 7 Angstroms in this example, '''Figure 11'''.

[[Image:QM-define.png|thumb|center|800px|'''Figure 11'''. QM region defined. ]]

11). After defining the QM region, we then need to define the size of the active region. Again MolCluster helps us by estimating the number of atoms for a range of radii. Molecules not included in the active region, will be in the Frozen region. Fir this example, we shall define the specify active region to have a radius of 11 Angstroms, '''Figure 12'''.

[[Image:Active-region .png|thumb|center|800px|'''Figure 12'''. Radius of active region specified. ]]

12). Finally, we are asked to specify the output directory where all our files will be placed, and the basename for each of our clusters. In this example the output directory will be ''BMIM_MESO4_EXAMPLE/example'' and the base name will be ''cluster'', '''Figure 13'''.

[[Image:Ouput-filenames.png|thumb|center|800px| ]]

13). MolCluster then sets about creating the clusters according to our specifications. The terminal output for the first cluster (cluster_1) is shown in '''Figure 14'''. After creating all the clusters, MolCluster will terminate.

[[Image:cluster_1.png|thumb|center|800px|'''Figure 14'''. Cluster_1 created. ]]

14). Within the named output directory, each cluster has it's own subdirectory: cluster_1, cluster_2 etc. Within each of the subdirectories can be found the requested output files, '''Figure 15'''.

[[Image:directory-files.png|thumb|center|1100px|'''Figure 15'''. Output files. ]]

15). The file called system_info.txt summarises key information relating to the cluster. This is shown in '''Figure 16''' for cluster 1. We can see that in total there are 72 molecules (36 cations and 36 anions) and that, as requested, the total charge of the system is zero.

[[Image:system-info-cluster_1.png|thumb|center|800px|'''Figure 16'''. Total system information for cluster 1. ]]

*To find out how many molecules in the QM and active regions, we can open the file called ''molcluster.log'' in the parent directory. This is a record of all the options we selected. By scrolling through we can find the information relating to cluster 1, '''Figure 17''', and can see that there are 9 molecules in the QM region; 4 cations and 5 anions, resulting in a total charge of -1. There are 35 molecules in the active region.

[[Image:molcluster-log-cluster1-annot.png|thumb|center|800px|'''Figure 17'''. Information about cluster 1, found in the output file molcluster.log. ]]

*Returning to the files in our subdirectory ''cluster_1'', we can open ''cluster.xyz'' (or ''cluster_tiered.xyz'') in VMD to visualise the cut cluster, '''Figure 18''' for our cluster 1. ''cluster_tiered.xyz'' is particularly useful, as it allows us to visualise each of the distinct regions. All of the atoms in the QM region are labelled with a 1 (active labelled with 2 and frozen labelled with 3), therefore we can choose to visualise the QM region only, '''Figure 19a'''. In '''Figure 19b''', all the regions are shown in different colours.

[[Image:full-cluster-1.png|thumb|center|800px|'''Figure 18'''. Cluster 1 visualised in VMD. ]]

[[Image:cluster_tiered-edit.png|thumb|center|800px|'''Figure 19'''. '''(a)''' QM region visualised in VMD. '''(b)''' All regions, visualised in different colours. ]]

----

=Cutting Embedded Cluster=
*Embedded clusters are generated in two steps
*First a cluster of specific radius is generated using MolCLuster and Chemshell
1. Load MolClusterV2.3: ./MolCluster.py

2. Enter the directory containing the FIELD and HISTORY files as in the previous case

3. Select option [4] to Generate ChemShell input for cutting embedded cluster

4. then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.
After this you can choose the step at which the clusters are to be cut

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then see a number of options from which you can specify the exact atom number/type.

6. Enter the radius (in Angstroms) of the embedded cluster(s) to be cut

7. Enter the projected radius (in Angstroms) of the active regions ( this can be any value < embedded cluster radius)

8. Then enter the charge margin - distance (in Angstroms) from the cluster boundary to the outer point charges [[File:Embedded2.png]]

9. enter the number of added point charges. This is calculated from the charge density; (4 * density * density + 2)

10. enter the symbol to represent point charge 'X'

11.Specify the output directory

12. The output directory will haven inputs 'embedded_cluster_n', if chosen 'n' in step 4 and an embedded_cluster_specs.obj file

13. Upload the directory to cx1 login shell

14. In each of the 'embedded_cluster_n' will contain a 'bulk_fragment.chm' having the coordinates

15. generate bulk.pun from bulk_fragment.chm by loading chemshell 'module load chemshell mpi' and 'chemsh.x bulk_fragment.chm'

16. submit the job using the submit script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt_embedded.sh link]

*In the second step, clusters with different regions (QM and MM) with point charges outside are cut using MolCluster

17. When the job is finished transfer the folder to the local machine with MolClusterV2.3

18. Load MolClusterV2.3: ./MolCluster.py

19. Enter the same directory containing the FIELD and HISTORY files as given in the first step

20. select option [5] to cut cluster and add point charges

21. MolCluster will ask for the directory containing 'embedded_cluster_specs.obj' of the embedded cluster(s) generated by ChemShell. (the folder containing ChemSehll output)

22. Now the cluster specifications will be asked for. enter 'Y' if you want to use the same radius for the regions as entered before or 'N' if want to change the radius

23.In the next step MolCluster will ask for the type of QM region you want to specify
-->[S] Spherical region centred about the origin
-->[M] By number of total molcules closest to the origin
-->[A] By an upper limit of total atoms closest to the origin
-->[N] Specific number of molecules closest to the origin of each molecule type
-->[C] Custom region
-->[O] Spherical volumes centred about one or more user-defined origins

24. Clusters will be cut at this point and saved to the folder having the 'embedded_cluster_specs.obj' file.

::* open embedded_cluster_n, it will have the opt.chm, ff. dat and embedded_cluster_n.chm

25. transfer the folder to cx1

26. load chemshell on cx1 and run

<pre>module load chemshell mpi
chemsh.x embedded_cluster_n.chm</pre>

* embedded_cluster_n.pun will be generated

27. open opt.chm and edit the first line "dl-find coords=embedded_cluster_n.pun\". Also make changes in the opt.chm as described in [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link] and run the optimization

28. The submit script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt_embedded2.sh link]

==='''OLD instructions that relate to MolCluster v1-7'''===

1. Create a directory within the main MolCluster directory. Put the required HISTORY and FIELD files here.

2. Load MolCluster: ./MolCluster.py

3. Requests directory name to be specified (this is the location of the FIELD and HISTORY files). After specifying, the code will attempt to read and give an overview of the system.

4. First select option 2 to cut clusters, then you will be asked to identify the mechanism for choosing the clusters to cut, giving n or c:
::*'''[n]''': Cut a cluster every "nth" configuration. N.B: numbering starts from 1 (i.e. 1st timestep). Therefore, if you request n=1000, clusters for configurations 1, 1001, 2001 etc. will be created.
::*'''[c]''': Select a custom set of configurations i.e. you can specify exactly which configurations you want.
After this you can choose the step at which the clusters are to be cut

5. Once the configurations have been extracted, you will be asked to choose how the origin will be defined in the clusters to be cut. Options are:
::*'''[AN]''': Atom number
::*'''[AT]''': Atom type
::*'''[MN]''': Molecule number
::*'''[MT]''': Molecule type
::*'''[C]''': Custom coordinates

You will then see a number of options from which you can specify the exact atom number/type.

6. MolCluster will estimate the number of atoms within a region, for a range of radii with respect to your origin. Use this information to help you decide on the total radius (in Angstroms) of the clusters to be cut. You will be asked to specify this.

7. MolCluster has two options for deciding which molecules to include/exclude at the boundary of the clusters being cut:
::*'''[H]''': Hard boundary - all atoms of a molecule must be within the cutoff radius for the molecule to be included.
::*'''[S]''': Soft boundary - if the centre of mass of a molecule is within the cutoff radius, the molecule will be included.

8. Specify if the clusters are required to be neutral ('''Y/N''').

9. Decide on the output formats:
::*'''[C]''': Generates a ChemShell fragment input file, with accompanying .xyz co-ordinates file.
::*'''[X]''': Generates the .xyz co-ordinates file only.

If '''[X]''' selected, the clusters will be cut, .xyz files generated and MolCluster will terminate.

If '''[C]''' selected, you will be asked if you would also like to generate the necessary ChemShell input files for a QM/MM optimisation ('''Y/N''').

10. If your answer to step 9 was '''[C]''' (generate a ChemShell fragment input) and '''Y''' (generate ChemShell input files for a QM/MM optimisation), you will then be asked to define the QM region. Available options are:
::*'''[S]''': Spherical region (or threshold) centred about the defined origin (although not necessarily spherical??!!)
:::: If '''[S]''' selected, MolCluster will estimate the number of atoms in regions defined by a range of radii. Specify the QM radius. This must be specified (in Angstroms) and must, obviously, be less than, or equal to, the total radius of the cluster. Soft boundary conditions are implemented.
::*'''[M]''': By number of molecules. Molecules closest to the origin will be included.
::*'''[A]''': By an upper limit of atoms. Only whole molecules & those closest to the origin included.
::*'''[C]''': Custom region i.e. can select molecules individually to be in the QM region
::*'''[O]''': Spherical regions centred about one or more origins

If options '''[C]''' or '''[O]''' selected, MolCluster will go straight to steps 11 and 12. Once the active region and the directory/filenames have been defined, MolCluster will then ask for the custom QM regions to be defined ''per'' cluster (see step 14).

NOTE: there can be a central active QM region (C), an active MM region (SA) and a frozen MM region (SF) (Figure I), so far you have selected the maximum radius for the size of the cluster, now select the radius of the active MM smaller than this.

[[File:Figure I.png]]

11. MolCluster will estimate the number of atoms that would be in the active and frozen regions for a range of active radii. This information can be used to help decide upon an appropriate active radius, specified (in Angstroms) and must, be less than, or equal to, the total radius of the cluster. If all atoms are to be included, simply enter "ALL". Soft boundary conditions are implemented.

12. Specify the output directory (i.e. where your final clusters and associated files will be saved) and specify the base-name for the output files (e.g. if you type "cluster" here, your clusters will be saved as cluster_1, cluster_2 etc.). NOTE: if you are going to use the trajectory_analysis scripts later the base filename must be "cluster".

13. Unless in step 10 above you selected options '''[C'''] or '''[O]''' (in which case, see point 14), MolCluster will generate the specified clusters and then terminate.

14. If option '''[C]''' was selected in step 10, MolCluster will at this point list all the molecules in the first cluster, along with the distances to the origin. You will be asked to list all the molecules to be included in the QM region for this cluster. The same procedure is carried out for each cluster, before the clusters are generated and MolCluster terminates.

If option '''[O]''' was selected in step 10, you will be asked to specify how many region centers you employed in setting up a non-spherical QM region.
You can choose the centre of the multiple regions via atom/molecule or use the current cluster origin. A table is provided to help you make this choice identifying atom numbers and molecules and their distance from the cluster origin.

----
::*To run ChemShell in Cartesian coordinate (MolCluster1.7):

::*open opt.chm and delete the lines:
coordinates=hdlc \
residues=
::* then run
module load chemshell/3.5.0
chemsh.x cluster_n.chm
*follow the same steps as in the previous case

----

Talk:Mod:Hunt Research Group/ChemShell files

2018-02-21T11:48:32Z

Klw14: /* cluster_1.chm */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 63 73 75 93 125 126 127 128 }\
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=lanl2dz basisspec={ { lanl2dz * } } ecpspec={ { lanl2dz * } }
g98_mem=640000000 charge=-3 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=300\
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122 123 124 125 126 127 128 } } } \
active_atoms = { 1 2 4 5 6 7 9 14 15 17 20 22 24 26 27 29 30 31 37 38 39 40 43 46 47 48 53 56 58 59 63 65 67 69 70 73 74 75
78 79 83 85 87 89 91 92 93 94 96 97 99 100 103 105 106 107 108 110 111 113 117 118 120 121 122 125 126 127 128 }\
list_option = full \
maxcycle = 800\
restart = yes \
dump = 1 \
result = cluster_opt.pun

</pre>

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters.

An example ff.dat file is shown below for an La NaCl system.

<pre>
vdw NA NA 87.5812212 14750.8882
vdw NA CL 522.364248 593182.84
vdw CL CL 3106.1365 24120183.2
vdw LA CL 1471.76193 6991022.6
vdw LA NA 284.384407 228931.111
vdw LA LA 667.42017 1856038.3
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

To generate the parameters for the ff.dat file some work needs to be completed!

I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.

To generate the C6 value needed the calculation needed is 4*E*sigma^6
To generate the C12 value needed the calculation needed is 4*E*sigma^12

These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.

To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.chm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/ChemShell files

2018-02-21T11:48:05Z

Klw14: /* ff.dat */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 63 73 75 93 125 126 127 128 }\
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=lanl2dz basisspec={ { lanl2dz * } } ecpspec={ { lanl2dz * } }
g98_mem=640000000 charge=-3 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=300\
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122 123 124 125 126 127 128 } } } \
active_atoms = { 1 2 4 5 6 7 9 14 15 17 20 22 24 26 27 29 30 31 37 38 39 40 43 46 47 48 53 56 58 59 63 65 67 69 70 73 74 75
78 79 83 85 87 89 91 92 93 94 96 97 99 100 103 105 106 107 108 110 111 113 117 118 120 121 122 125 126 127 128 }\
list_option = full \
maxcycle = 800\
restart = yes \
dump = 1 \
result = cluster_opt.pun

</pre>

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters.

An example ff.dat file is shown below for an La NaCl system.

<pre>
vdw NA NA 87.5812212 14750.8882
vdw NA CL 522.364248 593182.84
vdw CL CL 3106.1365 24120183.2
vdw LA CL 1471.76193 6991022.6
vdw LA NA 284.384407 228931.111
vdw LA LA 667.42017 1856038.3
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

To generate the parameters for the ff.dat file some work needs to be completed!

I took the E and sigma values from my MD simulation using the LJ potential and completed a couple of transformations to ensure the correct values were being used. First I had to change E and sigma to C6 and C12 values.

To generate the C6 value needed the calculation needed is 4*E*sigma^6
To generate the C12 value needed the calculation needed is 4*E*sigma^12

These values are in kJ but we need kCal here, so each value is then multiplied by 0.239006 to get values in kCal.

To ensure this process was correct I took Asiwaryas FIELD file from the MD and completed the above calculations. I then compared the values I obtained and the values in the ff.dat she was using and found no difference.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.hm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2018-02-19T13:20:25Z

Klw14:

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.chm, ff.dat and cluster_1.chm files to the hpc.
::the cluster_1.chm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.chm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and ecp sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. When editing tcl files it is important to first make a copy of the file calling it XXXX_original this way no matter what happens you have a copy to start from again! The second important thing is to count the brackets, you have not got to the end of a section if more brackets have been opened than have been closed. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets.

 LINK TO MY GAUSSIAN.TCL FILE 

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2018-02-19T13:01:36Z

Klw14: /* Step 2 - Editing input files */

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.chm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.chm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.chm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and ecp sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. When editing tcl files it is important to first make a copy of the file calling it XXXX_original this way no matter what happens you have a copy to start from again! The second important thing is to count the brackets, you have not got to the end of a section if more brackets have been opened than have been closed. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets.

 LINK TO MY GAUSSIAN.TCL FILE 

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2018-02-19T13:01:09Z

Klw14:

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.hm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.chm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.chm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and ecp sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. When editing tcl files it is important to first make a copy of the file calling it XXXX_original this way no matter what happens you have a copy to start from again! The second important thing is to count the brackets, you have not got to the end of a section if more brackets have been opened than have been closed. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets.

 LINK TO MY GAUSSIAN.TCL FILE 

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Mod:Hunt Research Group/calendar

2017-12-15T13:36:16Z

Klw14:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Not Done)
| Ken (Done)
| Becky (Not Done)
|-
| Sophie (Not Done)
| Lennart (Not Done)
| Oxana (Not Done)
|-
| Sanha (Not Done)
| Nerissa (Not Done)
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away

Lennart in South Africa

Oxana away
|19th
Sophie Away

Lennart in South Africa

Oxana away
|20th
Sophie Away

Lennart in South Africa

Oxana away
|21st
Sophie Away

Lennart in South Africa

Oxana away
|22nd
Sophie Away

Lennart in South Africa

Oxana away

Ken Away
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open

Tricia Away

Lennart in South Africa

Oxana away

Ken Away
|3rd
Tricia Away

Lennart in South Africa

Oxana away

Ken Away
|4th
Tricia Away

Lennart in South Africa

Oxana away

Ken Away
|5th
Tricia Away

Lennart in South Africa

Ken Away
| style="background: grey;" |6th
| style="background: grey;" |7th
|-
|8th Jan
|9th
|10th
|11th
|12th
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|8th
|9th
|10th
|11th
|12th
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|15th
|16th
|17th
|18th
|19th
| style="background: grey;" |20th
| style="background: grey;" |21st
|-
|22nd
|23rd
|24th
|25th
|26th
| style="background: grey;" |27th
| style="background: grey;" |28th
|-
|29th
|30th
|31st
| style="background: yellow;" |1st Feb
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
|8th
|9th
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
|13th
|14th
|15th
|16th
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
|20th
|21st
|22nd
|23rd
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
|27th
|28th
| style="background: yellow;" |1st Mar
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
|8th
|9th
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
|13th
|14th
|15th
|16th
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
|20th
|21st
|22nd
|23rd
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
|27th
|28th
|29th College Closed
|30th College Closed
Good Friday
| style="background: grey;" |31st
| style="background: yellow;" |1st Apr
Easter Sunday
|-
|}

Mod:Hunt Research Group/calendar

2017-12-15T13:32:28Z

Klw14:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia
| Ken (Not Done)
| Becky (Done)
|-
| Sophie
|Lennart
|
|-
|
|
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away

Lennart in South Africa

Oxana away
|19th
Sophie Away

Lennart in South Africa

Oxana away
|20th
Sophie Away

Lennart in South Africa

Oxana away
|21st
Sophie Away

Lennart in South Africa

Oxana away
|22nd
Sophie Away

Lennart in South Africa

Oxana away
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open

Tricia Away

Lennart in South Africa

Oxana away
|3rd
Tricia Away

Lennart in South Africa

Oxana away
|4th
Tricia Away

Lennart in South Africa

Oxana away
|5th
Tricia Away

Lennart in South Africa
| style="background: grey;" |6th
| style="background: grey;" |7th
|-
|8th Jan
|9th
|10th
|11th
|12th
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|8th
|9th
|10th
|11th
|12th
| style="background: grey;" |13th
| style="background: grey;" |14th
|-
|15th
|16th
|17th
|18th
|19th
| style="background: grey;" |20th
| style="background: grey;" |21st
|-
|22nd
|23rd
|24th
|25th
|26th
| style="background: grey;" |27th
| style="background: grey;" |28th
|-
|29th
|30th
|31st
| style="background: yellow;" |1st Feb
|2nd
| style="background: grey;" |3rd
| style="background: grey;" |4th
|-
|5th
|6th
|7th
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Mod:Hunt Research Group/MoltenSaltSimulation

2017-11-17T10:57:29Z

Klw14: /* Checking the system is equilibrated */

==Setting up and running Molten Salt Molecular Dynamic Simulations==

There are several pieces of information needed before staring any MD simulation

#The density of the system at the final temperature as it is used to determine the size of the simulation box
#Parameters for the Field File
#Potential to use in the Field File

Once the information is found, the input structure can be generated.

MD simulations on Molten Salts should be ran from a crystal structure. I don't know where to find crystal structures

===Using Packmol to generate starting configurations===

The density of the salt at the final temperature is needed to determine the box size for the simulation. The size of the simulation box can be determined by employing the following equation.

Volume = molar mass / 0.6022 (density / number of molecules)

Taking the cube root of the volume gives the length of the box size.

For each molecule considered in the MD simulation an input structure needs to be generated. These files need to have a the name ‘FILENAME.xyz’. For chlorine the .xyz file looks like this

<pre>
1
cl
CL 0.00000 0.00000 0.00000
</pre>

Once the input structure files are generated (one for each ion/molecule in the system) another file needs to be created which is the generation file that packmol uses. The generation file needs the size of the box, so it should have already been determined. The packmol generation file has to be named ‘FILENAME.inp’.

<pre>
#
# Generation of NACL
#

tolerance 3.0
filetype xyz
output nacl_200ips.xyz

structure na.xyz
number 200
inside box -10. -10. -10. 10. 10. 10.
end structure

structure cl.xyz
number 200
inside box -10. -10. -10. 10. 10. 10.
end structure
</pre>

The tolerance is....

Output nacl_200ips.xyz is the name of the file that is generated by packmol.

Structure na.xyz reads the molecular structure in the file na.xyz

Number 200 packs 200 Na atoms (can be moleculaes) into the box.

Inside box -10. -10. -10. 10. 10. 10. is the size of the box that is generated. On a grid the axes are drawn from -10 to 10, meaning the length of each side of the box is 20 Å.

End structure tells packmol that is everything that needs to be known for that particular molecule. The same process the occurs for the Cl ions.

====Running Packmol from the Terminal====

This is a relatively simple step!
Start in the same directory as the .inp and the .xyz files. From here navigate to the directory where packmol is stored. On my Mac it is in Applications.

../../../../Applications/packmol/packmol <FILENAME.inp

doing this will run packmol and generate a file with the name specified in the .inp file (nacl_200ips.xyz).

Its now necessary to move the newly generated .xyz file to the hpc, this can be done using the scope command in the terminal. Each MD simulation that is run needs to have its own directry, as all the files are called the same thing.

===Crystal Structures===

===Making the CONFIG file===
====Converting Packmol to CONFIG====

Once the file is on the HPC it is necessary to get the file into the correct format for dlpoly to read. To change the file format a perl conversion script, conv_xyz2conf.pl, needs to be used.

Conversion script is shown below for an NaCl system

<pre>
#!/usr/bin/perl

$name=$ARGV[0];
$i=1;
open(PDB,"${name}.xyz");
while($line=<PDB>){
if($line=~/ NA /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
if($line=~/ CL /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
}
open(CFG,">${name}.cfg");
$header="Converted from Packmol XYZ\n";
print CFG $header;
printf CFG "%10d%10d%10d%20.6f\n",0,0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;

for($i=1;$i<=$#atomType;$i++){
printf CFG "%-8s%10d\n",$atomType[$i],$i;
printf CFG "%20.6f%20.6f%20.6f\n",$atomX[$i],$atomY[$i],$atomZ[$i];
}
close(CFG); close(PDB);

</pre>

For each new system being considered the conversion script needs to be modified. Below is the section that needs to be modified.

<pre>
if($line=~/ NA /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
</pre>

For each ion/molecule in the system this section needs to be in the conversion scirpt. So for NaCl there will be this section twice, once with NA on the first line, the second time with CL on the first line.

To run the conversion script on the HPC simply type ‘perl conv_xyz2conf.pl FILENAME’, without .xyz.

Once the conversion script has run a new file is generate, named FILENAME.cfg. Change this file name to CONFIG.

====CONFIG file====

The CONFIG file will look something like this

<pre>
Converted from Packmol XYZ
0 0 0 0.000000
0.000000000000 0.000000000000 0.000000000000
0.000000000000 0.000000000000 0.000000000000
0.000000000000 0.000000000000 0.000000000000
NA 1
-2.187765 3.553628 0.510867
NA 2
0.656191 -5.190594 -3.045550
NA 3
-8.111144 -7.639522 5.169185
…
…
…
</pre>

It is necessary to modify the top section of the CONFIG file. The CONFIG file is hugely format driven, changing a 0 to 20 means that its necessary to remove both a 0 and a space.

The number 0 indicated that for each atom in the simulation there is 1 piece of information, its location. This number does change if additional information is known for each atom.

The number 1 idicates cubic boundary conditions.

The 400 indicates the number of ions in the simulation, 200 Na and 200 Cl.

The final number 0.0000 is the energy of the system. It is 0 because it hasn't yet been determined.

The next 3 lines of the file indicate the box size. The box size is 10% larger than that generated in packmol. This is done to ensure that all atoms are housed within the box, packmol can generate a system with the end of a molecule (although not considered here) hanging out the edge of the box. The size increase is continued as it is good practice to allow the system to expand if needed in the initial steps.

After that are the atomic coordinates.

Once the top few lines of the CONFIG file is modified it should look something like this.

<pre>
Converted from Packmol XYZ
0 1 400 0.000000
22.000000000000 0.000000000000 0.000000000000
0.000000000000 22.000000000000 0.000000000000
0.000000000000 0.000000000000 22.000000000000
NA 1
-2.187765 3.553628 0.510867
NA 2
0.656191 -5.190594 -3.045550
NA 3
-8.111144 -7.639522 5.169185
…
</pre>

The next steps involve setting up the files that are used by DL_poly. The CONFIG file has already been generated, the other 2 files that ned to be generated at the FIELD file and the CONTROL file. The FIELD file is normally made from values found in the literature. The CONTROL file tells DL_poly what to run.

===FIELD File===

The first line in the FIELD file is the title, although I havent done it here, I’d recommend that the reference for the parameters used later in the file are inculded in the title line. This will allow you to look back at the work years later and easily find the paper.

The second line is simply the unit of the calculation.

molecules shows the number of molecules that are considered in the system, in NaCl there are 2 types, Na and Cl.

The next section is about each molecule/atom in the simulation.
The name of the atom (NA)
The number of NA atoms in the simulation (200)
The number of atoms in the molecule (1)
Atomic mass and charge (22.98... 1.00... 1)
Finish – end of section on Na
Same for Cl

vdW3 – the number of non-bonded interactions

The next section contains the parameters and the potential (BHM) being employed

<pre>
900 NACL at 1200.00 K
units kJ
molecules 2
NA
nummols 475
atoms 1
NA 22.9898000000 1.00000 1
finish
CL
nummols 475
atoms 1
CL 35.4530000000 -1.00000 1
finish
vdW 3
CL CL BHM 0.26370 0.317 2.340 1.05 0.499
NA NA BHM 0.21096 0.317 2.755 6.99 8.68
CL NA BHM 0.15822 0.317 3.170 72.4 145.4
close
</pre>

===CONTROL File===

Probably need some explanation of what things are rather than sending people to the manual

<pre>
dlpoly run
temperature 600.00
ensemble nve
integrator leapfrog
steps 60000
equilibration 20000
scale 100
print 100
stack 100
stats 100
timestep 0.005
cutoff 15.000
delr 0.500
rvdw 7.600
ewald precision 1.0E-6
traj 1 10 0
job time 1000000.0
close time 1000.0
finish
</pre>

The information for the control file can be found in the DL_poly user manual. The version of Dlpoly being employed here is dlpoly 2.19.

During equilibration a gross rescaling outside of the thermostat is set by scale, perhaps best not used, can be used with a restart to scale the velocities to the required temperature.
Only use restart in a production run, monitor the temperature/energy for no large jumps!

cutoff is long range coloumb?? and rvdw is short range vow the cutoff, the manual is very unclear about what these are exactly, this is when long range vdw is set to zero, this generates a discontinuity as the function is cut-off, but maximum half box size, advantages to making this smaller has simulation runs faster, a minimum value 3-4 lj radius, but ideally this should be larger ... one should also set this to the same value as that for which the potential was developed!

printing options for the states, storage requirements are an issue, files can get very large, so set these 100-200 to start with. In equilibration you are just checking for equilibration for production.
more important is the traj command as this stores the trajectory and will influence the rdf evaluated by outside software, water use 10 but water is dynamic has low viscosity and moves very quickly for ionic liquids use larger number say 100 or larger.

===Submitting a simulation===

To submit jobs the submission script (Dlrun.sh) is employed. To run the script you need to be in the directory with the CONTROL, CONFIG, FIELD and Dlrun.sh files. Using the terminal simply type ‘qsub Dlrun.sh’ and enter.

Submission script for DL_POLY

Within the submission script it is possible to edit the number of processors and the amount of memory that is required.

===Visualising the Output===

Right click on the XQuartz icon (back X with an orange ring around its centre) and open a terminal, via the applications tab. In this new terminal window sign into the HPC and navigate to the directory containing the simulation.

Once in the directory type
module load vmd
vmd

This will launch VMD via the HPC, so it isnt necessary to instal VMD on your local machine. Although it is always useful to have!

Once VMD has opened select ‘New Molecule’ from the ‘File’ tab at the top left and browse to find the HISTORY file. Change the file type to ‘DLPOLY V2 History’. If you don’t select the correct file type the program will freeze and you’ll need to start the whole procedure again.

Once the HISTORY file and correct file type are selected click load. On the black display screen there should be lots of small dots moving around. To change the size of the atoms to something that is more visible click on the ‘Graphics’ tab and select representations. Using the ‘Drawing Method’ drop down list select CPK.

===Procedure===

 EACH SIMULATION NEEDS TO BE IN IT'S OWN DIRECTORY

The initial CONFIG file can be run at a temperature of about 300K. In the 'Getting started: generating a solvated structure and "relaxing" it' section of the Wiki, it is advised that the first run should be at 5K. As we are dealing with molten salts that don't melt until several hundred degrees, we can start at a higher temperature. The first run employs the NVE ensemble and is relatively short 500 steps and ensures that the parameters being employed are sensible, if they are not then the simulation will run into problems.

The next simulation run has been carried out above the melting temperature, 1200K, again employing the NVE ensemble. This run is longer at 60000 steps meaning 500ps with a tilmestep of 0.005. The starting CONFIG file has been generated from the REVCON file from the short run at 300K. The REVCON file needs to be renamed as CONFIG and the temperature in the CONTROL file changed.

Next a simulation employing the NVT ensemble has been carried out, again at 1200K using the REVCON file from the 1200K NVE simulation. This enables the size of the box to change accounting for the different temperatures that are being used.

Following the NPT simulation, the temperature is increased by 100K, to 1300K where an NVE simulation is carried out. The REVCON file from the 1200K NPT simulation is the new CONFIG file.

Starting at 1200K an NVE simulation followed by an NPT simulation has been completed. The temperature is then increased by 100K and an NVE followed by NPT simulation is completed. The CONTROL file is not changed, other than the temperature and the type of ensemble. This is repeated until the temperature is well above the melting point of the salt.

===Checking the system is equilibrated===

There are 3 sections that need to be commonly checked for basic analysis that should be carried out at the end of each simulation.

First thing to check is the energy of the system. Is The energy getting to a stable value before the ensemble freezes it in an NVE simulation?
The second thing is the temperature. This will always vary, but should remain within 10% (ideally 5%) of the set value in an NPT simulation.
The final thing to check in an NPT is the volume of the box. Has the volume changed and remains constant during the NPT simulation.

To get the data points to plot the graphs needed for the above checks a very useful script has been written by Vincent. [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/statis2xmgr] To get the script simply copy it from the link and save it as a new file call statis2xmgr.

to run the script simply type './statis2xmgr 1' this will give the energy data points in a file called stat2dl. It is necessary to change the file name to something else as each time you run the script it calls the file the same thing, overwriting what was there before. Typing no number at all after the script name gives the options available, temperature is 2 and volume is 19. To plot the points generated using statis2xmgr you can use gun plot. gnu plot is very powerful and I only ever use it to plot a scatter graph, ensuring the temp / energy / volume is not misbehaving. To ue gnu plot type 'gnu plot' in the HPC terminal, this will run gnuplot. then type "plot 'filename' " (you need the apostrophes) and it will plot that data and a popup will appear.

Calculating RDF

The method I am currently using is the in-built RDF from DL_poly.

In the CONTROL file simply type 'rdf' and 'print rdf' this will calculate and write a new file called RDFDAT. To bring the RDFDAT file back the submission script might need to be modified.

Modifying Dlrun.sh

simply include this line towards the end of the submission script (with all the other that look the same)

cp $TMPDIR/RDFDAT $PBS_O_WORKDIR/

This will copy the RDFDAT file back to your directory from the HPC where the calculation was completed.

====Points to consider====

Sometimes when you have modified a file and resubmit the calculations it appears that the modifications that you have made have not occurred. This is because the HPC only reads the files every minute or so, it is worth modifying the files, waiting a minute or two then re-submitting the modified file.

For the work I have carried out finding reliable parameters for the FIELD file caused some major issues. I expect most of the parameters being used come from literature. If this is the case it is worth trying to find multiple papers with the same parameters, or at east very similar. Many papers say they use parameters from paper X, but is worth trying to find two papers that state the parameters and not just reference them. I found that there are commonly problems in reporting the parameters in the correct units!

With a KCl system voids kept forming in the simultation box. I thought this would be due to problems with the parameters being used in the FIELD file.
I tried several different sets of parameters, all to no avail.
I tried changing the density (within what I could find in literature) which didn’t work.
Eventually I tried taking a NaCl simulation that was working and changing the Na ions to K ions. It seems that the packmol structure generated, even for differeny box sizes (accounting for the different densities), didn’t change enough to allow the simulation to be succesful.

To change the Na ions to K the following command was used.
‘sed –i ‘s/NA/K /’ FILENAME’
you should notice that there is a space after the K, this is because DL_poly is very format driven. Replacing ‘Na’ with ‘K’ only replaces 1 of the 2 characters being removed.

Mod:Hunt Research Group/MoltenSaltSimulation

2017-11-17T10:56:25Z

Klw14: /* Checking the system is equilibrated */

==Setting up and running Molten Salt Molecular Dynamic Simulations==

There are several pieces of information needed before staring any MD simulation

#The density of the system at the final temperature as it is used to determine the size of the simulation box
#Parameters for the Field File
#Potential to use in the Field File

Once the information is found, the input structure can be generated.

MD simulations on Molten Salts should be ran from a crystal structure. I don't know where to find crystal structures

===Using Packmol to generate starting configurations===

The density of the salt at the final temperature is needed to determine the box size for the simulation. The size of the simulation box can be determined by employing the following equation.

Volume = molar mass / 0.6022 (density / number of molecules)

Taking the cube root of the volume gives the length of the box size.

For each molecule considered in the MD simulation an input structure needs to be generated. These files need to have a the name ‘FILENAME.xyz’. For chlorine the .xyz file looks like this

<pre>
1
cl
CL 0.00000 0.00000 0.00000
</pre>

Once the input structure files are generated (one for each ion/molecule in the system) another file needs to be created which is the generation file that packmol uses. The generation file needs the size of the box, so it should have already been determined. The packmol generation file has to be named ‘FILENAME.inp’.

<pre>
#
# Generation of NACL
#

tolerance 3.0
filetype xyz
output nacl_200ips.xyz

structure na.xyz
number 200
inside box -10. -10. -10. 10. 10. 10.
end structure

structure cl.xyz
number 200
inside box -10. -10. -10. 10. 10. 10.
end structure
</pre>

The tolerance is....

Output nacl_200ips.xyz is the name of the file that is generated by packmol.

Structure na.xyz reads the molecular structure in the file na.xyz

Number 200 packs 200 Na atoms (can be moleculaes) into the box.

Inside box -10. -10. -10. 10. 10. 10. is the size of the box that is generated. On a grid the axes are drawn from -10 to 10, meaning the length of each side of the box is 20 Å.

End structure tells packmol that is everything that needs to be known for that particular molecule. The same process the occurs for the Cl ions.

====Running Packmol from the Terminal====

This is a relatively simple step!
Start in the same directory as the .inp and the .xyz files. From here navigate to the directory where packmol is stored. On my Mac it is in Applications.

../../../../Applications/packmol/packmol <FILENAME.inp

doing this will run packmol and generate a file with the name specified in the .inp file (nacl_200ips.xyz).

Its now necessary to move the newly generated .xyz file to the hpc, this can be done using the scope command in the terminal. Each MD simulation that is run needs to have its own directry, as all the files are called the same thing.

===Crystal Structures===

===Making the CONFIG file===
====Converting Packmol to CONFIG====

Once the file is on the HPC it is necessary to get the file into the correct format for dlpoly to read. To change the file format a perl conversion script, conv_xyz2conf.pl, needs to be used.

Conversion script is shown below for an NaCl system

<pre>
#!/usr/bin/perl

$name=$ARGV[0];
$i=1;
open(PDB,"${name}.xyz");
while($line=<PDB>){
if($line=~/ NA /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
if($line=~/ CL /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
}
open(CFG,">${name}.cfg");
$header="Converted from Packmol XYZ\n";
print CFG $header;
printf CFG "%10d%10d%10d%20.6f\n",0,0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;
printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;

for($i=1;$i<=$#atomType;$i++){
printf CFG "%-8s%10d\n",$atomType[$i],$i;
printf CFG "%20.6f%20.6f%20.6f\n",$atomX[$i],$atomY[$i],$atomZ[$i];
}
close(CFG); close(PDB);

</pre>

For each new system being considered the conversion script needs to be modified. Below is the section that needs to be modified.

<pre>
if($line=~/ NA /){
chomp($line);
@data=split(/ +/,$line);
$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];
$i++;
}
</pre>

For each ion/molecule in the system this section needs to be in the conversion scirpt. So for NaCl there will be this section twice, once with NA on the first line, the second time with CL on the first line.

To run the conversion script on the HPC simply type ‘perl conv_xyz2conf.pl FILENAME’, without .xyz.

Once the conversion script has run a new file is generate, named FILENAME.cfg. Change this file name to CONFIG.

====CONFIG file====

The CONFIG file will look something like this

<pre>
Converted from Packmol XYZ
0 0 0 0.000000
0.000000000000 0.000000000000 0.000000000000
0.000000000000 0.000000000000 0.000000000000
0.000000000000 0.000000000000 0.000000000000
NA 1
-2.187765 3.553628 0.510867
NA 2
0.656191 -5.190594 -3.045550
NA 3
-8.111144 -7.639522 5.169185
…
…
…
</pre>

It is necessary to modify the top section of the CONFIG file. The CONFIG file is hugely format driven, changing a 0 to 20 means that its necessary to remove both a 0 and a space.

The number 0 indicated that for each atom in the simulation there is 1 piece of information, its location. This number does change if additional information is known for each atom.

The number 1 idicates cubic boundary conditions.

The 400 indicates the number of ions in the simulation, 200 Na and 200 Cl.

The final number 0.0000 is the energy of the system. It is 0 because it hasn't yet been determined.

The next 3 lines of the file indicate the box size. The box size is 10% larger than that generated in packmol. This is done to ensure that all atoms are housed within the box, packmol can generate a system with the end of a molecule (although not considered here) hanging out the edge of the box. The size increase is continued as it is good practice to allow the system to expand if needed in the initial steps.

After that are the atomic coordinates.

Once the top few lines of the CONFIG file is modified it should look something like this.

<pre>
Converted from Packmol XYZ
0 1 400 0.000000
22.000000000000 0.000000000000 0.000000000000
0.000000000000 22.000000000000 0.000000000000
0.000000000000 0.000000000000 22.000000000000
NA 1
-2.187765 3.553628 0.510867
NA 2
0.656191 -5.190594 -3.045550
NA 3
-8.111144 -7.639522 5.169185
…
</pre>

The next steps involve setting up the files that are used by DL_poly. The CONFIG file has already been generated, the other 2 files that ned to be generated at the FIELD file and the CONTROL file. The FIELD file is normally made from values found in the literature. The CONTROL file tells DL_poly what to run.

===FIELD File===

The first line in the FIELD file is the title, although I havent done it here, I’d recommend that the reference for the parameters used later in the file are inculded in the title line. This will allow you to look back at the work years later and easily find the paper.

The second line is simply the unit of the calculation.

molecules shows the number of molecules that are considered in the system, in NaCl there are 2 types, Na and Cl.

The next section is about each molecule/atom in the simulation.
The name of the atom (NA)
The number of NA atoms in the simulation (200)
The number of atoms in the molecule (1)
Atomic mass and charge (22.98... 1.00... 1)
Finish – end of section on Na
Same for Cl

vdW3 – the number of non-bonded interactions

The next section contains the parameters and the potential (BHM) being employed

<pre>
900 NACL at 1200.00 K
units kJ
molecules 2
NA
nummols 475
atoms 1
NA 22.9898000000 1.00000 1
finish
CL
nummols 475
atoms 1
CL 35.4530000000 -1.00000 1
finish
vdW 3
CL CL BHM 0.26370 0.317 2.340 1.05 0.499
NA NA BHM 0.21096 0.317 2.755 6.99 8.68
CL NA BHM 0.15822 0.317 3.170 72.4 145.4
close
</pre>

===CONTROL File===

Probably need some explanation of what things are rather than sending people to the manual

<pre>
dlpoly run
temperature 600.00
ensemble nve
integrator leapfrog
steps 60000
equilibration 20000
scale 100
print 100
stack 100
stats 100
timestep 0.005
cutoff 15.000
delr 0.500
rvdw 7.600
ewald precision 1.0E-6
traj 1 10 0
job time 1000000.0
close time 1000.0
finish
</pre>

The information for the control file can be found in the DL_poly user manual. The version of Dlpoly being employed here is dlpoly 2.19.

During equilibration a gross rescaling outside of the thermostat is set by scale, perhaps best not used, can be used with a restart to scale the velocities to the required temperature.
Only use restart in a production run, monitor the temperature/energy for no large jumps!

cutoff is long range coloumb?? and rvdw is short range vow the cutoff, the manual is very unclear about what these are exactly, this is when long range vdw is set to zero, this generates a discontinuity as the function is cut-off, but maximum half box size, advantages to making this smaller has simulation runs faster, a minimum value 3-4 lj radius, but ideally this should be larger ... one should also set this to the same value as that for which the potential was developed!

printing options for the states, storage requirements are an issue, files can get very large, so set these 100-200 to start with. In equilibration you are just checking for equilibration for production.
more important is the traj command as this stores the trajectory and will influence the rdf evaluated by outside software, water use 10 but water is dynamic has low viscosity and moves very quickly for ionic liquids use larger number say 100 or larger.

===Submitting a simulation===

To submit jobs the submission script (Dlrun.sh) is employed. To run the script you need to be in the directory with the CONTROL, CONFIG, FIELD and Dlrun.sh files. Using the terminal simply type ‘qsub Dlrun.sh’ and enter.

Submission script for DL_POLY

Within the submission script it is possible to edit the number of processors and the amount of memory that is required.

===Visualising the Output===

Right click on the XQuartz icon (back X with an orange ring around its centre) and open a terminal, via the applications tab. In this new terminal window sign into the HPC and navigate to the directory containing the simulation.

Once in the directory type
module load vmd
vmd

This will launch VMD via the HPC, so it isnt necessary to instal VMD on your local machine. Although it is always useful to have!

Once VMD has opened select ‘New Molecule’ from the ‘File’ tab at the top left and browse to find the HISTORY file. Change the file type to ‘DLPOLY V2 History’. If you don’t select the correct file type the program will freeze and you’ll need to start the whole procedure again.

Once the HISTORY file and correct file type are selected click load. On the black display screen there should be lots of small dots moving around. To change the size of the atoms to something that is more visible click on the ‘Graphics’ tab and select representations. Using the ‘Drawing Method’ drop down list select CPK.

===Procedure===

 EACH SIMULATION NEEDS TO BE IN IT'S OWN DIRECTORY

The initial CONFIG file can be run at a temperature of about 300K. In the 'Getting started: generating a solvated structure and "relaxing" it' section of the Wiki, it is advised that the first run should be at 5K. As we are dealing with molten salts that don't melt until several hundred degrees, we can start at a higher temperature. The first run employs the NVE ensemble and is relatively short 500 steps and ensures that the parameters being employed are sensible, if they are not then the simulation will run into problems.

The next simulation run has been carried out above the melting temperature, 1200K, again employing the NVE ensemble. This run is longer at 60000 steps meaning 500ps with a tilmestep of 0.005. The starting CONFIG file has been generated from the REVCON file from the short run at 300K. The REVCON file needs to be renamed as CONFIG and the temperature in the CONTROL file changed.

Next a simulation employing the NVT ensemble has been carried out, again at 1200K using the REVCON file from the 1200K NVE simulation. This enables the size of the box to change accounting for the different temperatures that are being used.

Following the NPT simulation, the temperature is increased by 100K, to 1300K where an NVE simulation is carried out. The REVCON file from the 1200K NPT simulation is the new CONFIG file.

Starting at 1200K an NVE simulation followed by an NPT simulation has been completed. The temperature is then increased by 100K and an NVE followed by NPT simulation is completed. The CONTROL file is not changed, other than the temperature and the type of ensemble. This is repeated until the temperature is well above the melting point of the salt.

===Checking the system is equilibrated===

There are 3 sections that need to be commonly checked for basic analysis that should be carried out at the end of each simulation.

First thing to check is the energy of the system. Is The energy getting to a stable value before the ensemble freezes it in an NVE simulation?
The second thing is the temperature. This will always vary, but should remain within 10% (ideally 5%) of the set value in an NPT simulation.
The final thing to check in an NPT is the volume of the box. Has the volume changed and remains constant during the NPT simulation.

To get the data points to plot the graphs needed for the above checks a very useful script has been written by Vincent. [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/statis2xmgr] To get the script simply copy it from the link and save it as a new file call statis2xmgr.

to run the script simply type './statis2xmgr 1' this will give the energy data points in a file called stat2dl. It is necessary to change the file name to something else as each time you run the script it calls the file the same thing, overwriting what was there before. Typing no number at all after the script name gives the options available, temperature is 2 and volume is 19. To plot the points generated using statis2xmgr you can use gun plot. gnu plot is very powerful and I only ever use it to plot a scatter graph, ensuring the temp / energy / volume is not misbehaving. To ue gnu plot type 'gnu plot' in the HPC terminal, this will run gnuplot. then type plot 'filename' and it will plot that data and a popup will appear.

Calculating RDF

The method I am currently using is the in-built RDF from DL_poly.

In the CONTROL file simply type 'rdf' and 'print rdf' this will calculate and write a new file called RDFDAT. To bring the RDFDAT file back the submission script might need to be modified.

Modifying Dlrun.sh

simply include this line towards the end of the submission script (with all the other that look the same)

cp $TMPDIR/RDFDAT $PBS_O_WORKDIR/

This will copy the RDFDAT file back to your directory from the HPC where the calculation was completed.

====Points to consider====

Sometimes when you have modified a file and resubmit the calculations it appears that the modifications that you have made have not occurred. This is because the HPC only reads the files every minute or so, it is worth modifying the files, waiting a minute or two then re-submitting the modified file.

For the work I have carried out finding reliable parameters for the FIELD file caused some major issues. I expect most of the parameters being used come from literature. If this is the case it is worth trying to find multiple papers with the same parameters, or at east very similar. Many papers say they use parameters from paper X, but is worth trying to find two papers that state the parameters and not just reference them. I found that there are commonly problems in reporting the parameters in the correct units!

With a KCl system voids kept forming in the simultation box. I thought this would be due to problems with the parameters being used in the FIELD file.
I tried several different sets of parameters, all to no avail.
I tried changing the density (within what I could find in literature) which didn’t work.
Eventually I tried taking a NaCl simulation that was working and changing the Na ions to K ions. It seems that the packmol structure generated, even for differeny box sizes (accounting for the different densities), didn’t change enough to allow the simulation to be succesful.

To change the Na ions to K the following command was used.
‘sed –i ‘s/NA/K /’ FILENAME’
you should notice that there is a space after the K, this is because DL_poly is very format driven. Replacing ‘Na’ with ‘K’ only replaces 1 of the 2 characters being removed.

Mod:Hunt Research Group/calendar

2017-11-13T17:00:52Z

Klw14:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia
| Ken (Not Done)
| Becky (Done)
|-
| Sophie
|
|
|-
|
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|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|16th Oct
|17th
|18th
|19th
|20th
Ken Away
| style="background: grey;" |21st
| style="background: grey;" |22nd
|-
|23rd Tricia in Spain
|24th Tricia in Spain
|25th Tricia in Spain
|26th Tricia in Spain
|27th Tricia in Spain Oxana away
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|-
|4th Tricia in Germany
|5th Tricia in Germany
|6th Tricia in Germany
|7th Tricia in Germany
|8th Tricia in Germany
Ken Away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
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|18th
Sophie Away
|19th
Sophie Away
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Sophie Away
|21st
Sophie Away
|22nd
Sophie Away
| style="background: grey;" |23rd
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|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open
|3rd
|4th
|5th
| style="background: grey;" |6th
| style="background: grey;" |7th
|}

Mod:Hunt Research Group/calendar

2017-10-14T11:52:04Z

Klw14:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Not Done)
| Ken (Not Done)
| Becky (Not done)
|-
| Sophie (Not done)
|
|
|-
|
|
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|16th Oct
|17th
|18th
|19th
|20th
Ken Away
| style="background: grey;" |21st
| style="background: grey;" |22nd
|-
|23rd
|24th
|25th
|26th
|27th
| style="background: grey;" |28th
| style="background: grey;" |29th
|-
|30th
|31st
| style="background: yellow;" |1st Nov
|2nd
|3rd
| style="background: grey;" |4th
| style="background: grey;" |5th
|-
|6th
|7th
|8th
|9th
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|14th
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|28th
|29th
|30th
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| style="background: grey;" |2nd
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|-
|4th
|5th
|6th
|7th
|8th
Ken Away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11st
Ken Away
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|13th
|14th
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|-
|18th
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College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open
|3rd
|4th
|5th
| style="background: grey;" |6th
| style="background: grey;" |7th
|}

Mod:Hunt Research Group/calendar

2017-10-11T15:37:27Z

Klw14:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Not Done)
| Ken (Not Done)
| Becky (Not done)
|-
| Sophie (Not done)
|
|
|-
|
|
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|16th Oct
|17th
|18th
|19th
|20th
| style="background: grey;" |21st
| style="background: grey;" |22nd
|-
|23rd
|24th
|25th
|26th
|27th
| style="background: grey;" |28th
| style="background: grey;" |29th
|-
|30th
|31st
| style="background: yellow;" |1st Nov
|2nd
|3rd
| style="background: grey;" |4th
| style="background: grey;" |5th
|-
|6th
|7th
|8th
|9th
|10th
| style="background: grey;" |11th
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|14th
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|16th
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| style="background: grey;" |18th
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|23rd
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| style="background: grey;" |25th
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|-
|27th
|28th
|29th
|30th
| style="background: yellow;" |1st Dec
| style="background: grey;" |2nd
| style="background: grey;" |3rd
|-
|4th
|5th
|6th
|7th
|8th
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11st
|12th
|13th
|14th
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| style="background: grey;" |16th
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|-
|18th
|19th
|20th
|21st
|22nd
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open
|3rd
|4th
|5th
| style="background: grey;" |6th
| style="background: grey;" |7th
|}

Mod:Hunt Research Group

2017-09-22T13:16:00Z

Klw14: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#Using VPN from home, for Sierra follow the college instructions [[link]]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers - MacFusion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''installing Xcode'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]

*Using AIMALL: '''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]

*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]

*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
*'''MD Post processing'''
#Code to Recentre DL_PLOY HISTORY file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/recentre_xyz.py link]
#Link to the code to convert the DL_POLY HISTORY file to the multi-frame XYZ file[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/his2xyz.py link]

*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://www.ace-net.ca/wiki/Gaussian_Error_Messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Using a z-matrix [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#Using solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#
#Script to pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#General procedure for locating transition state structures [[link]]

===ADF General===
#Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]

===Codes to Help Analysis===
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Installing Packmol
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/calendar

2017-07-07T13:05:32Z

Klw14: /* Calendar */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Done)
| Nukorn (Done)
| Becky (Not done)
|-
| Richard (Not done)
| Ken (Done)
| Sophie (Done)
|-
| Mikkaila (Done)
| Lennart Frankemoelle (not done)
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
| style="background: yellow;" |5th June
|6th
|7th
|8th
|9th
| style="background: grey;" |10th
| style="background: grey;" |11th
|-
|12th
|13th
|14th
|15th
|16th
| style="background: grey;" |17th
| style="background: grey;" |18th
|-
|19th
|20th
|21st
|22nd
|23rd
| style="background: grey;" |24th
| style="background: grey;" |25th
|-
|26th
Mikkaila Away
|27th
|28th
Sophie Away
|29th
Sophie Away
|30th
Ken Away

Sophie Away

Mikkaila Away
| style="background: yellow;" |1st July
| style="background: grey;" |2nd
|-
|3rd
Ken Away
|4th
|5th
|6th
|7th
| style="background: grey;" |8th
| style="background: grey;" |9th
|-
|10th
Tricia Away
|11th
Tricia Away
|12th
Tricia Away
|13th
Tricia Away
|14th
Tricia Away
| style="background: grey;" |15th
| style="background: grey;" |16th
|-
|17th
Ken Away
Tricia Away
|18th
Sophie Away

Tricia Away
|19th
Tricia Away
|20th
Tricia Away
|21st
Tricia Away
| style="background: grey;" |22nd
| style="background: grey;" |23rd
|-
|24th
|25th
|26th
|27th
|28th
| style="background: grey;" |29th
| style="background: grey;" |30th

|-
|31st
| style="background: yellow;" |1st Aug

|2nd
|3rd
Tricia Away
|4th
Tricia Away
| style="background: grey;" |5th
| style="background: grey;" |6th
|-
|7th
Tricia Away
|8th
Tricia Away
|9th
Tricia Away
|10th
Tricia Away
|11th
Tricia Away
| style="background: grey;" |12th
| style="background: grey;" |13th
|-
|14th
Tricia Away
|15th
Tricia Away
|16th
|17th
|18th
| style="background: grey;" |19th
| style="background: grey;" |20th
|-
|21st
Ken Away
|22nd
Ken Away
|23rd
Ken Away
|24th
Ken Away
|25th
Ken Away

Nukorn Away
| style="background: grey;" |26th
| style="background: grey;" |27th
|-
|28th
BANK HOLIDAY
|29th
Ken Away

Mikkaila Away

Nukorn Away
|30th
Ken Away

Mikkaila Away

Nukorn Away
|31st
Mikkaila Away

Nukorn Away
| style="background: yellow;" |1st Sept
Mikkaila Away

Nukorn Away
| style="background: grey;" |2nd
| style="background: grey;" |3rd
|-
|4th
|5th
|6th
|7th
|8th
| style="background: grey;" |9th
| style="background: grey;" |10th
|-
|11th
Tricia Away
|12th
Tricia Away
|13th
Tricia Away

Nukorn Away
|14th
Nukorn Away
|15th
Nukorn Away
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Nukorn Away
|19ht
Nukorn Away
|20th
Nukorn Away
|21st
|22nd
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
|26th
|27th
|28th
|29th
| Style="background: grey;" |30th
|
|}

Talk:Mod:Hunt Research Group/ChemShell files

2017-06-28T16:04:37Z

Klw14: /* cluster_1.chm */

===opt.chm files===

An example of an opt.hm file can be seen below.

<pre>
dl-find coords=cluster.pun\
theory=hybrid: { coupling=shift \
cutoff = 20 \
qm_region = { 63 73 75 93 125 126 127 128 }\
qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=lanl2dz basisspec={ { lanl2dz * } } ecpspec={ { lanl2dz * } }
g98_mem=640000000 charge=-3 mult=1 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=300\
atom_types = { NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL
CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL CL LA } } \
groups = { { 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122 123 124 125 126 127 128 } } } \
active_atoms = { 1 2 4 5 6 7 9 14 15 17 20 22 24 26 27 29 30 31 37 38 39 40 43 46 47 48 53 56 58 59 63 65 67 69 70 73 74 75
78 79 83 85 87 89 91 92 93 94 96 97 99 100 103 105 106 107 108 110 111 113 117 118 120 121 122 125 126 127 128 }\
list_option = full \
maxcycle = 800\
restart = yes \
dump = 1 \
result = cluster_opt.pun

</pre>

Each of the 'keywords' are explains in the following table.

{| class="wikitable"
|-
! Keyword
! To Specify
|-
| dl_find
| optimisation library, recommended by ChemShell
|-
| coords= cluster.pun
| initial coordinates of system, found in cluster.pun
|-
| theory=hybrid:
| sets up a QM/MM model based on one QM and one MM region
|-
| cutoff
| cutoff for QM/MM electrostatic interactions, we assume this is angstroms
|-
| qm_region
| list of atoms in QM part, list the atoms from *.pun file
|-
| qm_theory=gaussian
| module used for QM energy and forces
|-
| mm_theory=dl_poly
| module used for MM energy and forces
|-
| mxexcl
| Allocation parameter for excluded atom list, may needs to be increased for large QM calculations - MAXIMUM number of excluded atoms per atom??
|-
| atom types
| atom type settings
|-
| groups
| specify a list of (ideally neutral) charge groups. A list of lists, each sublist containing the atom numbers of atom belonging to the group. Increase the accuracy of the electrostatic energy when using a cutoff
|-
| Active atoms
| Atoms that move, i think in the MM region
|-
| list_option
| how much output to generate
|-
| maxcycle
| maximum number of optimisation cycles
|-
| dump
| writes info every dump steps
|-
| restart
| restarts from dump file
|-
| result
| optimised coordinates
|-
|}

I know that these explanations are not very good, they come directly from the ChemShell manual. They can be found by googling chemshell followed by the keyword you want to know about

general info can be found http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/hyb_new.html

Dispersion can not be used for all elements, for example I can't get it to work for Lanthanum

Keyword dispersion_correction=gd3bj

=== ff.dat ===

Contains the MM parameters.

For LJ potential parameters use the keyword vdw. An example ff.dat file is shown below for an La NaCl system.

<pre>
declare NA
declare CL
declare LA
vdw NA NA 0.54392 2.350
vdw NA CL 0.48116 3.230
vdw CL CL 0.41840 4.450
vdw LA CL 0.32409 4.100
vdw LA NA 0.36952 3.050
vdw LA LA 0.25104 3.750
charge NA 1.000
charge CL -1.000
charge LA 3.000
</pre>

from the DL_Poly MD simulation I simply copied the FIELD file and pasted below the declare lines. At the start of each line from the FIELD file i put vdw and deleted LJ from the middle of each line.

I then manually included the charge section for each ion in the simulation.

=== cluster.pun ===

cluster_x.pun contains the coordinates, charges and connectivity of the cluster.

Example file

<pre>
block = fragment records = 0
block = title records = 1
molecule 1
block = coordinates records = 128
NA -1.17552336830323e+01 -2.25822336289483e+00 -7.41906688094151e+00
NA -1.13521549857055e+01 1.04974316157998e+01 3.17001647803856e+00
NA -6.73838733674510e+00 7.11482088811635e+00 1.56304961518929e+01
NA 7.22007866327388e+00 -6.84081052190736e-01 4.34920591606900e+00
...
...
block = atom_charges records = 128
1.0000000000
1.0000000000
1.0000000000
1.0000000000
...
...
block = connectivity records = 163
1 40
1 43
1 66
1 107
...
</pre>

It is important to check the connectivity records and ensure there are not bonds where you're not expecting them.

=== cluster_1.chm ===

generated by MolCluster and transferred to HPC. cluster_1.hm is used to generate the custer.pun file.

cluster_1.chm contains the atomic positions of all ions in the cluster cut by MolCluster.

The first line of this file will contain the following.

<pre>
c_create coords=cluster.pun
</pre>

This line tells chemshell to generate a file called cluster.pun using the coordinate in the file

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2017-06-27T15:29:51Z

Klw14:

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.hm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.hm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.hm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and ecp sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. When editing tcl files it is important to first make a copy of the file calling it XXXX_original this way no matter what happens you have a copy to start from again! The second important thing is to count the brackets, you have not got to the end of a section if more brackets have been opened than have been closed. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets.

 LINK TO MY GAUSSIAN.TCL FILE 

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2017-06-27T15:02:05Z

Klw14: /* Point charge position with Pseudopotentials */

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.hm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.hm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.hm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and ecp sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. When editing tcl files it is important to first make a copy of the file calling it XXXX_original this way no matter what happens you have a copy to start from again! The second important thing is to count the brackets, you have not got to the end of a section if more brackets have been opened than have been closed. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets. This did initially work for jobs employing dl-find, however it doesnt seem to have worked for single point energy jobs. I am still trying to rectify this problem.

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2017-06-27T14:38:04Z

Klw14:

=== Step 1 - Molcluster ===

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

=== Step 2 - Editing input files ===

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.hm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.hm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.hm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

== Errors that have been encountered ==

=== Point charge position with Pseudopotentials ===
As I have been trying to model an La ion in molten NaCl I need to employ a pseudo potential for my La ion. When trying to use an in-built PP, such as LanL2DZ the gaussian.com file has point charges between the basis set and eco sections. This resulted in ECP's not being included on the ions and the job would fail. The gaussian.log file included a large section with all ions having "No pseudo potential on this centre."

To overcome this problem it was necessary to edit the gaussian.tcl file in the ChemShell tcl directory. I searched for sections on ecp's and moved them (by copying and pasting) to just below sections on basis sets. This did initially work for jobs employing dl-find, however it doesnt seem to have worked for single point energy jobs. I am still trying to rectify this problem.

=== gaussian.update ===

In the opt.out file a section was included showing the following

<pre>
******************** DL_POLY Pairlist calculation requested ********************

hybrid: dl_poly updated OK
hybrid: Warning gaussian update failed
invalid command name "gaussian.update"
</pre>

This particular problem is that the gaussian.update section had not been specified in the gaussian.tcl file or the tclIndex file.

In the tclIndex file the following line needs to be on line number 371

<pre>
set auto_index(gaussian.update) [list source [file join $dir gaussian.tcl]]
</pre>

In the gaussian.tcl file the following need to the final section

<pre>
proc gaussian.update { args } {
return 0
}
</pre>

Talk:Mod:Hunt Research Group/Chemshell Step By Step

2017-06-27T14:26:06Z

Klw14: Created page with "== Step 1 - Molcluster == The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is requir..."

== Step 1 - Molcluster ==

The first thing that needs to be done to run any chemshell job is generate the input files. To cut the clusters a successful MD simulation is required and MolCluster needs to be installed.

For information on how to obtain, install and run MolCluster, read [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster here].

== Step 2 - Editing input files ==

The next stage of the process is editing the input files to do what you want them to do. From the MolCluster directory on your local machine you need to copy the opt.hm, ff.dat and cluster_1.hm files to the hpc.
::the cluster_1.hm file might be named something else! the file will always end *_1.chm, *_2.chm *_3.chm etc.

The files need to be edited before you can run a ChemShell job.

:: ff.dat needs to contain the parameters from the MD simulation. This is not a simple copy and paste, the numbers needs by ChemShell are in kCal while the numbers often used in DL_poly are in kJ/mol

HOW DO YOU CHANGE BETWEEN THE TWO

:: the cluster_1.hm (created by MolCluster) file needs to become the cluster.pun (input file for ChemShell) file required by ChemShell. There are 2 methods to do this depending on the ChemShell code you are using. Both methods are explained on the Running ChemShell page [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell here]

:: opt.chm is essentially the control file. It contains all of the keywords and tells ChemShell what you want it to do.

Each of these files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files here]

Mod:Hunt Research Group

2017-06-27T14:11:18Z

Klw14: /* Running QM/MM Simulations in ChemShell */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers - MacFusion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
*'''MD Post processing'''
#Code to Recentre DL_PLOY HISTORY file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/recentre_xyz.py link]
#Link to the code to convert the DL_POLY HISTORY file to the multi-frame XYZ file[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/his2xyz.py link]

*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===Gaussian General===
#We are starting a database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# Here is an already existing database of common errors [https://www.ace-net.ca/wiki/Gaussian_Error_Messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Using a z-matrix [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#Using solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]
#Script to pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
#General procedure for locating transition state structures [[link]]

===ADF General===
#Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]

===Codes to Help Analysis===
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Installing Packmol
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:43:38Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file.
::*cluster.pun: coordinate, atom_charges and connectivity records

All input files are explained in the Explaining ChemShell files page from the Hunt Research Group wiki home page. The ff.dat is also explained in the Force Field Parameters page.

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link] alternatively if ChemShell is installed on your HPC account you can use the submission script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh_local-install here] 
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:34:23Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file.
::*cluster.pun: coordinate, atom_charges and connectivity records

All input files are explained in the Explaining ChemShell files page from the Hunt Research Group wiki home page. The ff.dat is also explained in the Force Field Parameters page.

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link] alternatively if ChemShell is installed on your HPC account you can use the submission script [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh_local-install here]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/submit opt.sh local-install

2017-06-27T10:32:59Z

Klw14: Created page with "<pre> #!/bin/sh #PBS -l walltime=300:00:00 #PBS -lselect=1:ncpus=16:mem=64000mb #PBS -j oe #PBS -q pqph module load dl_poly/2.19 module load mpi module load intel-suite/2016..."

<pre>

#!/bin/sh
#PBS -l walltime=300:00:00
#PBS -lselect=1:ncpus=16:mem=64000mb
#PBS -j oe
#PBS -q pqph

module load dl_poly/2.19
module load mpi
module load intel-suite/2016.3
module load gaussian/g09-d01
#module load chemshell/3.5.0

export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

cp $PBS_O_WORKDIR/opt.chm $TMPDIR/.
cp $PBS_O_WORKDIR/ff.dat $TMPDIR/.
cp $PBS_O_WORKDIR/cluster.pun $TMPDIR/.
cp $PBS_O_WORKDIR/*.chk $TMPDIR/.
cd $TMPDIR
/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x opt.chm > opt.out

cp $TMPDIR/cluster* /$PBS_O_WORKDIR/
cp $TMPDIR/dlf_* /$PBS_O_WORKDIR/
cp $TMPDIR/gaussian.* /$PBS_O_WORKDIR/
cp $TMPDIR/opt* /$PBS_O_WORKDIR/
cp $TMPDIR/path* /$PBS_O_WORKDIR/
cp $TMPDIR/param.defs /$PBS_O_WORKDIR/
cp $TMPDIR/hybrid* /$PBS_O_WORKDIR/

</pre>

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:25:25Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file.
::*cluster.pun: coordinate, atom_charges and connectivity records

All input files are explained in the Explaining ChemShell files page from the Hunt Research Group wiki home page. The ff.dat is also explained in the Force Field Parameters page.

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:18:36Z

Klw14:

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified [[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files| here]]
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:18:17Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified ][https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files| here]]
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:17:33Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files| here]
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-27T10:15:37Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster needs to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T16:04:29Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will need to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T16:00:29Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.

2. can be found by clicking gaussian, after following step 1.

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:48:25Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

{{font color|red|There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.
2. can be found by clicking gaussian, after following step 1.}}

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:46:43Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

red
There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.
2. can be found by clicking gaussian, after following step 1.

writing

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:46:08Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

red
There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.
2. can be found by clicking gaussian, after following step 1.
writing

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:44:11Z

Klw14:

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell 1 and the other is specific to gaussian 2. I can't seem to provide links!

1. can be found by looking on the ChemShell user manual homepage and clicking QM interfaces under the Energy/Gradient Evaluators heading on the left of screen.
2. can be found by clicking gaussian, after following step 1.

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:41:23Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] or the dedicated ChemShell Force Field Parameters Aqueous Cu(II) page from the wiki home page. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/quantum.html| here] and the other is specific to gaussian [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/gaussian.html| here].

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:37:38Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] and [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II)| here]. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/quantum.html| here] and the other is specific to gaussian [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/gaussian.html| here].

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:37:06Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] and [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II)| here]. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell [www.cse.scitech.ac.uk/ccg/software/chemshell/manual/quantum.html| here] and the other is specific to gaussian [www.cse.scitech.ac.uk/ccg/software/chemshell/manual/gaussian.html| here].

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:35:58Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] and [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II)| here]. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at for finding QM keywords. 1 page is a general page for all QM_theory that can be used in ChemShell [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/quantum.html| here] and the other is specific to gaussian [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/gaussian.html| here].

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:35:01Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] and [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II)| here]. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

There are 2 different pages to look at here. 1 page is a general page for all QM_theory that can be used in ChemShell [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/quantum.html| here] and the other is specific to gaussian [http://www.cse.scitech.ac.uk/ccg/software/chemshell/manual/gaussian.html| here]. Between the two you should be able to find all the keywords you need for controlling the QM region

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]

Talk:Mod:Hunt Research Group/ChemShell

2017-06-22T15:30:32Z

Klw14: /* Input for ChemShell */

== Input for ChemShell ==

*To run a QM/MM optimisation, three input files are required:
opt.chm
cluster.pun
ff.dat

::*ff.dat : the forcefield in ChemShell format - ff.dat files are explained [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files#ff.dat| here] and [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II)| here]. The ff.dat file generated in MolCluster need to be edited! 
::*opt.chm: ChemShell input file. Options for the ChemShell optimisation specified here.
::*cluster.pun: coordinate, atom_charges and connectivity records

::*as part of generating the "cut" cluster using MolCluster you will have generated a range files, e.g. check the directory "cluster_1", and the files you need now are cluster_1.chm, ff.dat and opt.hm

::*note that MolCluster has not generated cluster.pun, but has generated cluster_n.chm, the coordinates file, which is used to generate cluster.pun

*login to CX1 and copy your cluster directories over then ...

*To generate cluster.pun from cluster_n.chm, load ChemShell and then run cluster_n.chm directly on the cx1 login shell
<pre>module load chemshell mpi
chemsh.x cluster_n.chm</pre>
::*successful result will generate a file cluster.pun and the screen info will look like this:
<pre>
Initialising ChemShell 3.5.0 on linux
c_create/======================================== Tstep: 0.1 Ttot: 0.1 ==
ChemShell exiting code 0
</pre>

 UPDATE June 2017

Giuseppe has installed chemshell onto my HPC account, so I'm not using the chemshell code on the HPC available to everyone.

To generate the cluster.pun file copy the cluster_1.chm file generated by MolCluster to the HPC. Create a new file called cluster_pun_generate and paste the following into it.

<pre>
export TCLROOT=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/
export TCLLIBPATH=/work/$USER/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/tcl/
export TCL_LIBRARY=/work/$USER/tcl/tcl8.4.20___gcc_4.4.7/lib
export LD_LIBRARY_PATH=$TCL_LIBRARY:$LD_LIBRARY_PATH

/work/klw14/ChemShell/chemsh-3.5.0___intel-suite__2016.3___tcl8.4.20___gcc_4.4.7/bin/chemsh.x cluster_*.chm

</pre>

The lines in this script are specific to my file set up so make sure you are calling the correct files.

It is then important to give yourself permission to run the script. "chmod u+x cluster_pun_generate"

to run the script and generate the cluster.pun file type "./cluster_pun_generate"

 UPDATE END 

::'''NB''': check the connectivity in the cluster.pun
:add some more information on this
:if you have only water molecules there should be no issue, but if you have a solvated species spurious "connectivity" may occur.
:in the CuSO4 example ....
search for /conn
lines to remove, total number to change

EXAMPLE SECTION OF FILE

*edit the opt.chm according to the system under study
*open opt.chm and edit the 'qm_theory' options (nproc, scfconv, g98_mem, charge, multiplicity, basis set, method etc )
edit the number of nproc so it is one less than the number called by PBS
mocluster generates defaults, maxcyc should relate to the number of degrees of freedom, so g09 suggests 3N+20 so for 51 atoms =173)
memory is in bytes 1,000,000 is 1 MB.

LINK TO EXPLANATION

*you will beed to add conn and mxexcl options manually to this file after the mm_theory.
::*mxexcl depends on the QM region, in the chemshell manual this is "Allocation parameter for excluded atom list, may need to be increased for qm/mm calculations with a large qm region" please refer ChemShell manual for more details [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_manual link]
chemshell has a list of all the atoms, and those in the QM region need to be excluded from the MM computation
this number needs checking!! This relates to the number ...
::*conn=cluster.pun tells chemshell to read the connectivity from the cluster.pun file
::*for our example you will need to change ...

qm_theory=gaussian : { nproc=15 maxcyc=200 scfconv=5 basis=631gdp g98_mem=640000000 charge=0 mult=2 hamiltonian=b3lyp } \
mm_theory=dl_poly : { mm_defs=ff.dat \
conn=cluster.pun \
mxexcl=500 \
'''NB:''' please make sure that there is no space left after the backslash in every line. If there is any space after the '\', the job will be terminated
* the submit script , submit_opt.sh, to run ChemShell optimisation is here [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]
this script submit the job, note that only the xx file is redirected while the job is running all other files are only copied over at the termination
add a comment re maxcycle being changed as wall time is hard, it will kill the job
cuso4+water QM +x active +y frozen a maxcycl of x and wall time of y are a good option
*don't forget different ques have different waltzes, and the more processors you use the "more" time you have

::* to submit the job
<pre>
qsub submit_opt.sh
</pre>

*the ChemShell optimisation creates as set of checkpoint files, gaussian files and 'path' files along with the output 'opt.out'
*load 'path_active.xyz' in VMD to follow the optimisation

*'''To restart a job'''
::*rename the 'op.out' to 'opt.out-n' (n=1,2,3..), else the previous opt.out will be overwritten and will loose the data. Please maintain the format as 'opt.out-n', since the python script to analyse the data reads this file format
:*open opt.chm
::::*increase maxcyle at the end of the file and add 'restart = yes \' command as the second last line

list_option = full \
maxcycle = 1500 \
dump = 1 \
restart = yes \
result = cluster_opt.pun
::*edit the submit script to read the checkpoint files before submitting the job [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/submit_opt.sh link]

*Analysis of the ChemShell optimisation
::* A python utility has been developed by Vincent to extract the various contributions to the total QM/MM energy, atom-atom distances and other parameters from the ChemShell output
:::*Among the files generated 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' lists the number of each of the water oxygens in the first salvation shell (here for the first salvation shell of Cu along with the distance of each of the Ow from Cu) and 'n' is the cluster number [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Cu_OW_first_solvation link]
*To trace back the particular water molecule in the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' to the DL_POLY HISTORY file, first map it to the Ow atom number in the opt.chm
*To map the Ow number to that in opt.chm, go to 'active_atoms' in opt.chm
<pre>active_atoms = { 1 2 3 4 5 6 7 8 9 13 14 15 16 17 18 31 32 33 52 53 54 55 56 57 58 59 60 61 62 63 67 68 69 73 74 75 76 77 78 79 80 81 85 86 87 88 89 90 </pre>
*bring the curser to '{'
*say for example the Ow number from the 'n_Cu_OW_first_solvation_shell_init_and_final_dist.txt' is 163, type '163' and press 'w'
*It will give the Ow number in opt.chm (e.g365). to go back to '{', enter163 and press 'b'
*In the cluster folder has 'atom_no_mapping.txt' created by MolCluster, which contain a list of 'orig_atom_no' and ' new_atom_no'. 'orig_atom_no' is the number in the HISTORY file and 'new_atom_no' is the corresponding atom number in the opt.chm
*open 'atom_no_mapping.txt' and map the atom number '365' to 'orig_atom_no' list.
*e.g if the 'orig_atom_no' is '643', use '643' in the script to draw the path of the centre of mass of a molecule throughout an animation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsMapCoMoverTraj link]