ChemWiki - User contributions [en]

Mod:Hunt Research Group

2019-11-26T13:33:59Z

Dv4018:

==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]
#advice [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 use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources 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]
#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]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH 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 [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]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [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]

===Key Papers, References and Resources===
*'''Papers'''
#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]
*'''Notes'''
#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)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#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]

===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]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[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]
#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]
#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]

===Gaussian Advanced===
#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]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 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]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#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]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii 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 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 each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_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]
# 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]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# 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]
#Simple script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [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 visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#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]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix 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]

*'''MOs'''
#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 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction 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]
#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]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/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]

===Running QM/MM Simulations in ChemShell===
==Tcl-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: Cu<sup>2+</sup> 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]
==Py-chemshell==

# Compiling Chemshell and required programs []
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Baisc QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

===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 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

2019-11-26T13:32:46Z

Dv4018:

==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]
#advice [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 use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources 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]
#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]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH 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 [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]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [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]

===Key Papers, References and Resources===
*'''Papers'''
#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]
*'''Notes'''
#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)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#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]

===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]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[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]
#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]
#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]

===Gaussian Advanced===
#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]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 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]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]
#Multidimensional Scans of Internal Coordinates [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Multidimensional_Scans_of_Internal_Coordinates link]

===Solvation===
#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]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii 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 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 each optimised step from a scan into xyz coordinate file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_scan_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]
# 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]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# 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]
#Simple script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [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 visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
#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]
#AIMAll 19.10.12 on iMacs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:AIMAllQuickFix 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]

*'''MOs'''
#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 Installation for an IMac [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction 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]
#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]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/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]

===Running QM/MM Simulations in ChemShell===
==Tcl-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: Cu<sup>2+</sup> 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]
==Py-chemshell==
# The DL_POLY_4 manual is available for download at this link [ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf]
# Compiling Chemshell and required programs []
# Molecular Mechanics computation with DL_POLY [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:_MM_Single_Point_computation]
# Baisc QM/MM single point and optimisations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation]
# Visualise optimisation trajectories in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Visualising_trajectories_with_VMD]
# Computing Mulliken charges and creating .wfn inputs for AIM analysis [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_Mulliken]

===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 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/Chemshell:Chemshell: Mulliken

2019-11-26T13:29:51Z

Dv4018:

When analysing QC optimisation results, it may be useful to compute Mulliken charges and/or perform an AIM analysis of the final structure. To do so, you have to perform a normal single point QM/MM analysis with a slight modification of the qm theory option:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1, properties=['mulliken', 'aimfile'])
</pre>

With the keyword argument "properties=['mulliken','aimfile]" we modify the input for NWChem so to perform the desired analysis. After running the .py script the WFN file will be generated in your directory with the name "_nwchem.wfn", while the Mulliken charges will be reported in the "_nwchem.out" file.

Mod:Hunt Research Group/Chemshell:Chemshell: Mulliken

2019-11-26T13:29:33Z

Dv4018: Created page with "When analysing QC optimisation results, it may be useful to compute Mulliken charges and/or perform an AIM analysis of the final structure. To do so, you have to perform a nor..."

When analysing QC optimisation results, it may be useful to compute Mulliken charges and/or perform an AIM analysis of the final structure. To do so, you have to perform a normal single point QM/MM analysis with a slight modification of the qm theory option:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1, properties=['mulliken', 'aimfile'])
<\pre>

With the keyword argument "properties=['mulliken','aimfile]" we modify the input for NWChem so to perform the desired analysis. After running the .py script the WFN file will be generated in your directory with the name "_nwchem.wfn", while the Mulliken charges will be reported in the "_nwchem.out" file.

Mod:Hunt Research Group/Chemshell:Chemshell: Visualising trajectories with VMD

2019-11-26T13:12:41Z

Dv4018: Created page with "Every time you run an optimisation with Chemshell a number of file will be crearted in the directory where the inputs are. Among these, the "path" files allow you to visualise..."

Every time you run an optimisation with Chemshell a number of file will be crearted in the directory where the inputs are. Among these, the "path" files allow you to visualise the optimisation path of the system during the computation. First of all, you have to download the "path_active.xyz" file from the HPC down to your PC using the scp command in the bash. Now you can open VMD and simply drag the .xyz file in the Main window and the whole trajectory of the active region will be visible in the Display window. You can change the representation with the Graphics option in the tool bar and see the optimisation evolution by pressing play on the right corner of the main window.

Mod:Hunt Research Group/Chemshell:Chemshell: QM/MM Single Point and optimisation

2019-11-26T12:42:20Z

Dv4018: Created page with "To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM..."

To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM computations. However, the molecules that are included in the QM region must not be 'counted' in the .ff file: if there are 3 molecules of water in the system and one is included in the QM region, the number of water molecules reported in the field file will be 2 (for DL_POLY: nummols=2).

The input files needed for this tutorial can be found at the following link:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM/MM_Single_Point_and_optimisation_inputs
</pre>

Most of the .py is the same as the one we used for the MM single point calculation. The first new line we can find is:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1)
</pre>

Here we have defined a new theory variable 'qm' in which we store information relative to the QM computations we want to perform. The class of the object determines the program that will be used for the QM computations. For each program chosen, we will have access to different arguments and argument values.
The first keyword 'method' defines the QC method we want to use; for the moment we will use Hartree-Fock (value "hf"). The B3LYP method can be called by assigning the value "b3lyp" to the method keyword argument and add the keyword argument "functional" (look at example below).

With the next keyword "basis" we set the basis set for the computation. In case you wanted to use a basis set that is not included in NWChem (or include an atom for which parameters are not available), you can import the basis set from an external file by adding the keyword argument "basis", e.g.:

<pre>
qm = NWChem(basis='(name of basis file).basis', method="dft", functional='b3lyp', charge=1, memory=380000, grid='ultrafine')
</pre>

In this example we have defined two optional arguments "grid='ultrafine'" and "memory=380000"; the former provides an additional specification for the input of NWChem, while the latter sets the memory usage for the computation. This last argument is required when submitting the job to the HPC.
The last keyword in this line is "charge" which sets the total charge of the QM region.

The MM theory line remains almost the same as for the MM single point: we only remove the fragment keyword as the initial configuration will be later defined.
Next, we find the line that defines the various parameters of the QM/MM computations:

<pre>
qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')
</pre>

The initial configuration is defined here with the frag keyword. The "qm_region" keyword lets us define the atoms we want included in the QM region (remember that indices start from 0 not 1!). With the "qm" and "mm" keywords we set the variables from which to take the information relative to the QM and MM part of the computations we want performed. "embedding" and "coupling" keywords are less important and for the moment you can use the provided values for your computations.

Moving down, we find a block of print statements. These have been included only to make the output include more information and are not necessary.

As with the MM computation, the file ends with the command setting the computation type. Try running the single point after having substituted the names of your input files where necessary.

Your output should look something like:

<pre>

**********************************************************************
QM energy = -532.960994138396 a.u.
MM energy = 0.020349646086 a.u.
QM/MM total energy = -532.940644492311 a.u.
**********************************************************************

Peak memory used by procedure chemsh.interfaces.qmmm.run: 149.508 MB

----------------------------------------------------------------------
Final SP energy = -532.940644492311 a.u.
----------------------------------------------------------------------
</pre>

Now uncomment the opt lines at the end of the .py file and run a QM/MM optimisation. If you want to save the output that you get on your terminal, launch chemshell like this:

<pre>
chemsh <name of .py file>.py > out
</pre>

Also in this case the optimisation is not supposed to converge with the maximum number of cycles set. Now, if you look into your directory a number of new files has been generated: the files whose name starts with _nwchem are the inputs and outputs of NWChem and are useful for debugging: when a problem arises in one of the involved programs you can directly check these files to find the error (the same goes for dl_poly inputs and outputs).

Mod:Hunt Research Group/Chemshell:Chemshell: QM/MM Single Point and optimisation inputs

2019-11-26T12:41:57Z

Dv4018: Created page with "Choose a name for each file and then insert it where needed in the .py file. The .pun file: <pre> block = fragment records = 0 block = title records = 1 Built with Pack..."

Choose a name for each file and then insert it where needed in the .py file.

The .pun file:

<pre>
block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
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CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
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CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
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CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
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HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
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HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0
</pre>

The .ff file:

<pre>
ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close
</pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

cluster = Fragment(coords='<name of .pun file>.pun', connmode=None)

qm = NWChem(method="hf", basis="3-21g", charge=-1)
mm = DL_POLY(ff='<name of .ff file>.ff', temperature=0.0)

qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')

print("### qmmm.qm_region =", qmmm.qm_region)
print("### qmmm.mm_region =", qmmm.mm_region)
print("### qmmm.mm.qmatoms =", qmmm.mm.qmatoms)
print("### qmmm.mm.mmatoms =", qmmm.mm.mmatoms)
print("### qmmm.mm.frag.names =", qmmm.qm.frag.natoms, qmmm.mm.frag.natoms)

#opt = Opt(active=[42, 67, 68, 69], theory=qmmm, maxcycle=100)
sp = SP(theory=qmmm, gradients=True)

#opt.run()
sp.run()

ecalc = sp.result.energyecalc = sp.result.energy
</pre>

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation

2019-11-14T14:24:30Z

Dv4018:

To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM computations. However, the molecules that are included in the QM region must not be 'counted' in the .ff file: if there are 3 molecules of water in the system and one is included in the QM region, the number of water molecules reported in the field file will be 2 (for DL_POLY: nummols=2).

The input files needed for this tutorial can be found at the following link:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM_Single_Point_and_optimisation_inputs
</pre>

Most of the .py is the same as the one we used for the single point calculation. The first new line we can find is:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1)
</pre>

Here we have defined a new theory variable 'qm' in which we store information relative to the QM computations we want to perform. The class of the object determines the program that will be used for the QM computations. For each program chosen, we will have access to different arguments and argument values.
The first keyword 'method' defines the functional we want to use; for the moment we will use Hartree-Fock (value "hf"). The B3LYP method can be called by assigning the value "b3lyp" to the method keyword argument.
With the next keyword "basis" we set the basis set for the computation. In case you wanted to use a basis set that is not included in NWChem (or include an atom for which parameters are not available), you can import the basis set from an external file (we will get into this in a later tutorial).
The last keyword in this line is "charge" with which we set the total charge of the QM region (the sum of the charges of all of the atom included).

The MM theory line remains almost the same as for the MM single point: we only remove the fragment keyword as the initial configuration will be specified somewhere else. Next, we find the line that defines the various parameters of the QM/MM computations:

<pre>
qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')
</pre>

The initial configuration is defined here with the frag keyword. The "qm_region" keyword lets us define the atoms we want included in the QM region (remember that indices start from 0 not 1!). With the "qm" and "mm" keywords we set the variables from which to take the information relative to the QM and MM part of the computations we want performed. "embedding" and "coupling" keywords are less important and for the moment you can use the provided values for your computations.

Moving down, we find a block of print statements. These have been included only to make the output include more information and are not necessary.

As with the MM computation, the file ends with the command setting the computation type. Try running the single point after having substituted the names of your input files where necessary.

Your output should look something like:

<pre>

**********************************************************************
QM energy = -532.960994138396 a.u.
MM energy = 0.020349646086 a.u.
QM/MM total energy = -532.940644492311 a.u.
**********************************************************************

Peak memory used by procedure chemsh.interfaces.qmmm.run: 149.508 MB

----------------------------------------------------------------------
Final SP energy = -532.940644492311 a.u.
----------------------------------------------------------------------
</pre>

Now uncomment the opt lines at the end of the .py file and run a QM/MM optimisation. If you want to save the output that you get on your terminal, launch chemshell like this:

<pre>
chemsh <name of .py file>.py > out
</pre>

Also in this case the optimisation is not supposed to converge with the maximum number of cycles set. Now, if you look into your directory a number of new files has been generated: the various file whose name starts with _nwchem are the inputs and outputs of NWChem and are useful for debugging (When a problem arises in one of the involved programs you can directly check these files to find the error).

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-14T14:15:23Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here: [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs MM Single Point Inputs]

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
</pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
</pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
</pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
</pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
</pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
</pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
</pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

The outputs that are generated by this computations are:
# _chemsh_run.log: a list of the times at which chemshell has been launched in that directory reporting the specific command used each time.
#CONFIG, FIELD, CONTROL, OUTPUT, REVCON, REVIVE and STATIS files are inputs and outputs of DL_POLY and will always be generated when DL_POLY is used.

The following outputs appear only if an optimisation is ran:

#"path" files report information on the optimisation trajectory. In an other tutorial we will show how to visualise optimisations in VMD using the "path.xyz" file.
#_dl_find.pun is the last configuration accepted during the optimisation. You can use this as an initial configuration to restart a crashed or incomplete optimisation.

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation inputs

2019-11-13T22:01:44Z

Dv4018:

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation inputs

2019-11-13T22:00:24Z

Dv4018: Created page with "Choose a name for each file and then insert it where needed in the .py file. The .pun file: <pre> block = fragment records = 0 block = title records = 1 Built with Pack..."

Choose a name for each file and then insert it where needed in the .py file.

The .pun file:

<pre>
block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0
</pre>

The .ff file:

<pre>
ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close
</pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

cluster = Fragment(coords='shell.pun', connmode=None)

qm = NWChem(method="hf", basis="3-21g", charge=-1)
mm = DL_POLY(ff='2rel_wat_8.ff', temperature=0.0)

qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')

print("### qmmm.qm_region =", qmmm.qm_region)
print("### qmmm.mm_region =", qmmm.mm_region)
print("### qmmm.mm.qmatoms =", qmmm.mm.qmatoms)
print("### qmmm.mm.mmatoms =", qmmm.mm.mmatoms)
print("### qmmm.mm.frag.names =", qmmm.qm.frag.natoms, qmmm.mm.frag.natoms)

#opt = Opt(active=[42, 67, 68, 69], theory=qmmm, maxcycle=100)
sp = SP(theory=qmmm, gradients=True)

#opt.run()
sp.run()

ecalc = sp.result.energyecalc = sp.result.energy
</pre>

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation

2019-11-13T21:50:17Z

Dv4018:

To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM computations. However, the molecules that are included in the QM region must not be 'counted' in the .ff file: if there are 3 molecules of water in the system and one is included in the QM region, the number of water molecules reported in the field file will be 2 (for DL_POLY: nummols=2).

The input files needed for this tutorial can be found at the following link:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM_Single_Point_and_optimisation_inputs
</pre>

Most of the .py is the same as the one we used for the single point calculation. The first new line we can find is:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1)
</pre>

Here we have defined a new theory variable 'qm' in which we store information relative to the QM computations we want to perform. The class of the object determines the program that will be used for the QM computations. For each program chosen, we will have access to different arguments and argument values.
The first keyword 'method' defines the functional we want to use; for the moment we will use Hartree-Fock (value "hf"). The B3LYP method can be called by assigning the value "b3lyp" to the method keyword argument.
With the next keyword "basis" we set the basis set for the computation. In case you wanted to use a basis set that is not included in NWChem (or include an atom for which parameters are not available), you can import the basis set from an external file (we will get into this in a later tutorial).
The last keyword in this line is "charge" with which we set the total charge of the QM region (the sum of the charges of all of the atom included).

The MM theory line remains almost the same as for the MM single point: we only remove the fragment keyword as the initial configuration will be specified somewhere else. Next, we find the line that defines the various parameters of the QM/MM computations:

<pre>
qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')
</pre>

The initial configuration is defined here with the frag keyword. The "qm_region" keyword lets us define the atoms we want included in the QM region (remember that indices start from 0 not 1!). With the "qm" and "mm" keywords we set the variables from which to take the information relative to the QM and MM part of the computations we want performed. "embedding" and "coupling" keywords are less important and for the moment you can use the provided values for your computations.

Moving down, we find a block of print statements. These have been included only to make the output include more information and are not necessary.

As with the MM computation, the file ends with the command setting the computation type. Try running the single point after having substituted the names of your input files where necessary.

Your output should look something like:

<pre>

**********************************************************************
QM energy = -532.960994138396 a.u.
MM energy = 0.020349646086 a.u.
QM/MM total energy = -532.940644492311 a.u.
**********************************************************************

Peak memory used by procedure chemsh.interfaces.qmmm.run: 149.508 MB

----------------------------------------------------------------------
Final SP energy = -532.940644492311 a.u.
----------------------------------------------------------------------
</pre>

Now uncomment the opt lines at the end of the .py file and run a QM/MM optimisation. If you want to save the output that you get on your terminal, launch chemshell like this:

<pre>
chemsh <name of .py file>.py > out
</pre>

Also in this case the optimisation is not supposed to converge with the maximum number of cycles set. Now, if you look into your directory a number of new files has been generated: the various file whose name starts with _nwchem are the inputs and outputs of NWChem and are useful for debugging (When a problem arises in one of the involved programs you can directly check these files to find the error).

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation

2019-11-13T21:49:29Z

Dv4018:

To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM computations. However, the molecules that are included in the QM region must not be 'counted' in the .ff file: if there are 3 molecules of water in the system and one is included in the QM region, the number of water molecules reported in the field file will be 2 (for DL_POLY: nummols=2).

The input files needed for this tutorial can be found at the following link:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM_Single_Point_and_optimisation_inputs
<\pre>

Most of the .py is the same as the one we used for the single point calculation. The first new line we can find is:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1)
<\pre>

Here we have defined a new theory variable 'qm' in which we store information relative to the QM computations we want to perform. The class of the object determines the program that will be used for the QM computations. For each program chosen, we will have access to different arguments and argument values.
The first keyword 'method' defines the functional we want to use; for the moment we will use Hartree-Fock (value "hf"). The B3LYP method can be called by assigning the value "b3lyp" to the method keyword argument.
With the next keyword "basis" we set the basis set for the computation. In case you wanted to use a basis set that is not included in NWChem (or include an atom for which parameters are not available), you can import the basis set from an external file (we will get into this in a later tutorial).
The last keyword in this line is "charge" with which we set the total charge of the QM region (the sum of the charges of all of the atom included).

The MM theory line remains almost the same as for the MM single point: we only remove the fragment keyword as the initial configuration will be specified somewhere else. Next, we find the line that defines the various parameters of the QM/MM computations:

<pre>
qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')
<\pre>

The initial configuration is defined here with the frag keyword. The "qm_region" keyword lets us define the atoms we want included in the QM region (remember that indices start from 0 not 1!). With the "qm" and "mm" keywords we set the variables from which to take the information relative to the QM and MM part of the computations we want performed. "embedding" and "coupling" keywords are less important and for the moment you can use the provided values for your computations.

Moving down, we find a block of print statements. These have been included only to make the output include more information and are not necessary.

As with the MM computation, the file ends with the command setting the computation type. Try running the single point after having substituted the names of your input files where necessary.

Your output should look something like:

<pre>

**********************************************************************
QM energy = -532.960994138396 a.u.
MM energy = 0.020349646086 a.u.
QM/MM total energy = -532.940644492311 a.u.
**********************************************************************

Peak memory used by procedure chemsh.interfaces.qmmm.run: 149.508 MB

----------------------------------------------------------------------
Final SP energy = -532.940644492311 a.u.
----------------------------------------------------------------------
<\pre>

Now uncomment the opt lines at the end of the .py file and run a QM/MM optimisation. If you want to save the output that you get on your terminal, launch chemshell like this:

<pre>
chemsh <name of .py file>.py > out
<\pre>

Also in this case the optimisation is not supposed to converge with the maximum number of cycles set. Now, if you look into your directory a number of new files has been generated: the various file whose name starts with _nwchem are the inputs and outputs of NWChem and are useful for debugging (When a problem arises in one of the involved programs you can directly check these files to find the error).

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-13T21:42:50Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs
</pre>

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
</pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
</pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
</pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
</pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
</pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
</pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
</pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

The outputs that are generated by this computations are:
# _chemsh_run.log: a list of the times at which chemshell has been launched in that directory reporting the specific command used each time.
#CONFIG, FIELD, CONTROL, OUTPUT, REVCON, REVIVE and STATIS files are inputs and outputs of DL_POLY and will always be generated when DL_POLY is used.

The following outputs appear only if an optimisation is ran:

#"path" files report information on the optimisation trajectory. In an other tutorial we will show how to visualise optimisations in VMD using the "path.xyz" file.
#_dl_find.pun is the last configuration accepted during the optimisation. You can use this as an initial configuration to restart a crashed or incomplete optimisation.

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-13T21:42:23Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs
</pre>

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
</pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
</pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
</pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
</pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
</pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
</pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
</pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

The outputs that are generated by this computations are:
# _chemsh_run.log: a list of the times at which chemshell has been launched in that directory reporting the specific command used each time.
#CONFIG, FIELD, CONTROL, OUTPUT, REVCON, REVIVE and STATIS files are inputs and outputs of DL_POLY and will always be generated when DL_POLY is used.

The following outputs appear only if an optimisation is ran:

#"path" files report information on the optimisation trajectory. In an other tutorial we will show how to visualise optimisations in VMD using the "path.xyz" file.
#:_dl_find.pun is the last configuration accepted during the optimisation. You can use this as an initial configuration to restart a crashed or incomplete optimisation.

Mod:Hunt Research Group/Chemshell:Chemshell: QM Single Point and optimisation

2019-11-13T21:42:20Z

To run a QM/MM computation we need do modify our .py file and define a new theory variable for the QM computations required. The .pun file will be the same we used for the MM computations. However, the molecules that are included in the QM region must not be 'counted' in the .ff file: if there are 3 molecules of water in the system and one is included in the QM region, the number of water molecules reported in the field file will be 2 (for DL_POLY: nummols=2).
The input files needed for this tutorial can be found at the following link:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_QM_Single_Point_and_optimisation_inputs
<\pre>

Most of the .py is the same as the one we used for the single point calculation. The first new line we can find is:

<pre>
qm = NWChem(method="hf", basis="3-21g", charge=-1)
<\pre>

Here we have defined a new theory variable 'qm' in which we store information relative to the QM computations we want to perform. The class of the object determines the program that will be used for the QM computations. For each program chosen, we will have access to different arguments and argument values.
The first keyword 'method' defines the functional we want to use; for the moment we will use Hartree-Fock (value "hf"). The B3LYP method can be called by assigning the value "b3lyp" to the method keyword argument.
With the next keyword "basis" we set the basis set for the computation. In case you wanted to use a basis set that is not included in NWChem (or include an atom for which parameters are not available), you can import the basis set from an external file (we will get into this in a later tutorial).
The last keyword in this line is "charge" with which we set the total charge of the QM region (the sum of the charges of all of the atom included).

The MM theory line remains almost the same as for the MM single point: we only remove the fragment keyword as the initial configuration will be specified somewhere else. Next, we find the line that defines the various parameters of the QM/MM computations:

<pre>
qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')
<\pre>

The initial configuration is defined here with the frag keyword. The "qm_region" keyword lets us define the atoms we want included in the QM region (remember that indices start from 0 not 1!). With the "qm" and "mm" keywords we set the variables from which to take the information relative to the QM and MM part of the computations we want performed. "embedding" and "coupling" keywords are less important and for the moment you can use the provided values for your computations.

Moving down, we find a block of print statements. These have been included only to make the output include more information and are not necessary.

As with the MM computation, the file ends with the command setting the computation type. Try running the single point after having substituted the names of your input files where necessary.

Your output should look something like:

<pre>

**********************************************************************
QM energy = -532.960994138396 a.u.
MM energy = 0.020349646086 a.u.
QM/MM total energy = -532.940644492311 a.u.
**********************************************************************

Peak memory used by procedure chemsh.interfaces.qmmm.run: 149.508 MB

----------------------------------------------------------------------
Final SP energy = -532.940644492311 a.u.
----------------------------------------------------------------------
<\pre>

Now uncomment the opt lines at the end of the .py file and run a QM/MM optimisation. If you want to save the output that you get on your terminal, launch chemshell like this:

<pre>
chemsh <name of .py file>.py > out
<\pre>

Also in this case the optimisation is not supposed to converge with the maximum number of cycles set. Now, if you look into your directory a number of new files has been generated: the various file whose name starts with _nwchem are the inputs and outputs of NWChem and are useful for debugging (When a problem arises in one of the involved programs you can directly check these files to find the error).

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-13T19:23:34Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs
</pre>

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
</pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
</pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
</pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
</pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
</pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
</pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
</pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

Mod:Hunt Research Group/Chemshell:Chemshell: MM Single Point computation inputs

2019-11-13T19:11:05Z

Dv4018:

Chose any name you like for the following files. The only thing that matters is the extension.

The .pun file:

<pre>

block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0

</pre>

The .ff file:

<pre>

ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close

</pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

reline = Fragment(coords="<name of pun file>.pun", connmode=None)
mm = DL_POLY(frag=reline, ff='name of ff file>.ff', temperature=0.0)

sp = SP(theory=mm)
sp.run()

#opt = Opt(theory=mm, maxcycle=100)
#opt.run()

</pre>

.

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-13T19:10:31Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs&veaction=edit
</pre>

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
</pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
</pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
</pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
</pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
</pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
</pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
</pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-13T19:09:04Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after logging in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

<pre>
https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Chemshell:Chemshell:_MM_Single_Point_computation_inputs&veaction=edit
<pre>

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are computing the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and files we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the meaning of the various commands it contains. Where necessary, fill in the name you chose for the various inputs. In what follows, is useful to remember that ChemShell is written in Python language. After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise your runscript will be useless.

Moving down we find:
<pre>
reline = Fragment(coords="<name of the pun file>.pun", connmode=None)
<pre>
Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:
<pre>
mm = DL_POLY(frag=reline, ff='<name of the field file>.ff', temperature=0.0)
<pre>
In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:
<pre>
sp = SP(theory=mm)
<pre>
Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

<pre>
sp.run()
<pre>

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

<pre>
chemsh <module name>.py
<pre>

At the end of the resulting output, you should get something like:

<pre>
>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec
<pre>

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the previous last two lines and uncomment the 'opt' lines. Save the changes to the script and run Chemshell again with the same command as before:

<pre>
chemsh <module name>.py
<pre>

In the 'opt' variable we use the keyword argument 'maxcycle' to set the maximum number of optimisation cycles.
Don't worry if the optimisation doesn't converge. It is not supposed to!

Mod:Hunt Research Group/Chemshell:Chemshell: MM Single Point computation inputs

2019-11-13T19:07:21Z

Dv4018:

Chose any name you like for the following files. The only thing that matters is the extension.

The .pun file:

<pre>

block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0

<pre>

The .ff file:

<pre>

ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close

<pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

reline = Fragment(coords="<name of pun file>.pun", connmode=None)
mm = DL_POLY(frag=reline, ff='name of ff file>.ff', temperature=0.0)

sp = SP(theory=mm)
sp.run()

#opt = Opt(theory=mm, maxcycle=100)
#opt.run()

<pre>

.

Mod:Hunt Research Group/Chemshell:Chemshell: MM Single Point computation inputs

2019-11-13T19:05:31Z

Dv4018:

Chose any name you like for the following files. The only thing that matters is the extension.

The .pun file:

<pre>

block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0

<pre>

The .ff file:

<pre>

ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close

<pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

reline = Fragment(coords="<name of pun file>.pun", connmode=None)
mm = DL_POLY(frag=reline, ff='name of ff file>.ff', temperature=0.0)

sp = SP(theory=mm)
sp.run()

#opt = Opt(theory=mm, maxcycle=100)
#opt.run()

<pre>

Mod:Hunt Research Group/Chemshell:Chemshell: MM Single Point computation inputs

2019-11-13T19:04:00Z

Dv4018:

Chose any name you like for the following files. The only thing that matters is the extension.

The .pun file:

<pre>

block = fragment records = 0
block = title records = 1
Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001
block = connectivity records = 0
<pre>

The .ff file:

<pre>

ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols 2
atoms 21
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CA 12.0107 -0.100 1
HA 1.00794 0.033 3
CS 12.0107 -0.131 1
HS 1.00794 0.068 2
NA 14.0067 0.791 1
CW 12.0107 0.132 1
HW 1.00794 0.034 2
OY 15.9994 -0.468 1
HY 1.00794 0.275 1
bonds 20
harm 1 2 680.0 1.099 0.0 0.0 # CA-HA
harm 1 3 680.0 1.099 0.0 0.0 # CA-HA
harm 1 4 680.0 1.099 0.0 0.0 # CA-HA
harm 1 16 980.0 1.498 0.0 0.0 # CA-NA
harm 5 6 680.0 1.099 0.0 0.0 # CA-HA
harm 5 7 680.0 1.099 0.0 0.0 # CA-HA
harm 5 8 680.0 1.099 0.0 0.0 # CA-HA
harm 5 16 980.0 1.498 0.0 0.0 # CA-NA
harm 9 10 680.0 1.099 0.0 0.0 # CA-HA
harm 9 11 680.0 1.099 0.0 0.0 # CA-HA
harm 9 12 680.0 1.099 0.0 0.0 # CA-HA
harm 9 16 980.0 1.498 0.0 0.0 # CA-NA
harm 13 16 980.0 1.516 0.0 0.0 # CS-NA
harm 13 14 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 15 680.0 1.0805 0.0 0.0 # CS-HS
harm 13 17 634.0 1.521 0.0 0.0 # CS-CW
harm 17 18 680.0 1.085 0.0 0.0 # CW-HW
harm 17 19 680.0 1.085 0.0 0.0 # CW-HW
harm 17 20 900.0 1.395 0.0 0.0 # CW-OY
harm 20 21 1106.0 0.949 0.0 0.0 # OY-HY
angles 37
harm 8 5 6 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 6 5 7 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 3 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 2 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 3 1 4 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 10 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 12 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 10 9 11 70.0 110.01 0.0 0.0 0.0 0.0 # HA-CA-HA
harm 8 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 6 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 7 5 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 2 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 3 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 4 1 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 12 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 10 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 11 9 16 70.0 108.90 0.0 0.0 0.0 0.0 # HA-CA-NA
harm 5 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 1 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 9 16 13 103.6 110.20 0.0 0.0 0.0 0.0 # CA-NA-CS
harm 16 13 14 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 15 70.0 106.40 0.0 0.0 0.0 0.0 # NA-CS-HS
harm 16 13 17 140.0 116.60 0.0 0.0 0.0 0.0 # NA-CS-CW
harm 13 17 18 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 19 70.0 108.30 0.0 0.0 0.0 0.0 # CS-CW-HW
harm 13 17 20 160.0 109.60 0.0 0.0 0.0 0.0 # CS-CW-OY
harm 14 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 15 13 17 70.0 109.30 0.0 0.0 0.0 0.0 # HS-CS-CW
harm 18 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 19 17 20 70.0 111.60 0.0 0.0 0.0 0.0 # HW-CW-OY
harm 17 20 21 70.0 110.90 0.0 0.0 0.0 0.0 # CW-OY-HY
harm 5 16 1 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 5 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 1 16 9 110.0 108.73 0.0 0.0 0.0 0.0 # CA-NA-CA
harm 14 13 15 70.0 108.60 0.0 0.0 0.0 0.0 # HS-CS-HS
harm 18 17 19 70.0 107.40 0.0 0.0 0.0 0.0 # HW-CW-Hw
dihedrals 52
cos3 17 13 16 5 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 1 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 17 13 16 9 0.100 0.550 0.650 0.5 0.5 0.0 0.0 # CW-CS-NA-CA
cos3 5 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 5 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 12 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 10 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 1 16 9 11 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 8 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 6 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 5 7 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 2 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 3 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 9 16 1 4 0.000 0.000 0.825 0.5 0.5 0.0 0.0 # CA-NA-CA-HA
cos3 13 16 5 8 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 6 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 5 7 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 2 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 3 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 1 4 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 12 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 10 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 13 16 9 11 0.000 0.000 0.940 0.5 0.5 0.0 0.0 # CS-NA-CA-HA
cos3 14 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 14 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 5 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 1 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 15 13 16 9 0.000 1.000 0.700 0.5 0.5 0.0 0.0 # HS-CS-NA-CA
cos3 20 17 13 16 -6.000 -5.000 3.200 0.5 0.5 0.0 0.0 # OY-CW-CS-NA
cos3 20 17 13 14 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 20 17 13 15 -0.500 -2.500 0.250 0.5 0.5 0.0 0.0 # OY-CW-CS-HS
cos3 18 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 19 17 13 16 -6.000 -7.000 0.750 0.5 0.5 0.0 0.0 # HW-CW-CS-NA
cos3 18 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 18 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 14 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 19 17 13 15 6.000 -3.000 2.000 0.5 0.5 0.0 0.0 # HW-CW-CS-HS
cos3 21 20 17 13 -0.356 -0.174 0.350 0.5 0.5 0.0 0.0 # HY-OY-CW-CS
cos3 21 20 17 18 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 21 20 17 19 -3.000 1.000 -2.000 0.5 0.5 0.0 0.0 # HY-OY-CW-HW
cos3 5 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CA-NA-CA-CA improper
cos3 13 16 5 1 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 5 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
cos3 13 16 1 9 0.000 2.000 0.000 0.5 0.5 0.0 0.0 # CS-NA-CA-CA improper
finish
Urea
nummols 3
atoms 8
C 12.0107 0.124 1
N 14.0067 -0.453 1
O 15.9994 -0.322 1
N 14.0067 -0.453 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
HT 1.00794 0.276 1
HC 1.00794 0.276 1
bonds 7
harm 1 2 980.0 1.335 0.0 0.0 # C-N
harm 1 3 1140.0 1.229 0.0 0.0 # C-O
harm 1 4 980.0 1.335 0.0 0.0 # C-N
harm 2 7 868.0 1.010 0.0 0.0 # N-HT
harm 2 8 868.0 1.010 0.0 0.0 # N-HC
harm 4 5 868.0 1.010 0.0 0.0 # N-HT
harm 4 6 868.0 1.010 0.0 0.0 # N-HC
angles 9
harm 2 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 2 1 4 140.0 114.20 0.0 0.0 0.0 0.0 # N-C-N
harm 4 1 3 160.0 122.90 0.0 0.0 0.0 0.0 # N-C-O
harm 1 2 7 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 2 8 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 1 4 5 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HT
harm 1 4 6 70.0 119.80 0.0 0.0 0.0 0.0 # C-N-HC
harm 5 4 6 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
harm 7 2 8 70.0 120.00 0.0 0.0 0.0 0.0 # HT-N-HC
dihedrals 11
cos3 3 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 3 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 7 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 4 1 2 8 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 5 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 2 1 4 6 0.0000 4.9000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-HT
cos3 7 2 1 8 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 5 4 1 6 0.0000 5.0000 0.0000 0.5 0.5 0.0 0.0 # HT-N-C-HC improper
cos3 3 1 2 4 0.0000 21.0000 0.0000 0.5 0.5 0.0 0.0 # O-C-N-N improper
finish
vdw 66
CS CS LJ 0.06600 3.50000
CS HS LJ 0.04450 3.01662
CS NA LJ 0.10592 3.37268
CS CA LJ 0.06600 3.50000
CS CW LJ 0.06600 3.50000
CS OY LJ 0.10592 3.27796
CS HA LJ 0.04450 2.95804
CS HW LJ 0.04450 2.77489
CS C LJ 0.10196 3.62284
CS O LJ 0.14419 3.21870
CS N LJ 0.12973 3.52491
HS HS LJ 0.03000 2.60000
HS NA LJ 0.07141 2.90689
HS CA LJ 0.04450 3.01662
HS CW LJ 0.04450 3.01662
HS OY LJ 0.07141 2.82524
HS HA LJ 0.03000 2.54951
HS HW LJ 0.03000 2.39165
HS C LJ 0.06874 3.12250
HS O LJ 0.09721 2.77417
HS N LJ 0.08746 3.03809
NA NA LJ 0.17000 3.25000
NA CA LJ 0.10592 3.37268
NA CW LJ 0.10592 3.37268
NA OY LJ 0.17000 3.15872
NA HA LJ 0.07141 2.85044
NA HW LJ 0.07141 2.67395
NA C LJ 0.16363 3.49106
NA O LJ 0.23141 3.10161
NA N LJ 0.20821 3.39669
CA CA LJ 0.06600 3.50000
CA CW LJ 0.06600 3.50000
CA OY LJ 0.10592 3.27796
CA HA LJ 0.04450 2.95804
CA HW LJ 0.04450 2.77489
CA C LJ 0.10196 3.62284
CA O LJ 0.14419 3.21870
CA N LJ 0.12973 3.52491
CW CW LJ 0.06600 3.50000
CW OY LJ 0.10592 3.27796
CW HA LJ 0.04450 2.95804
CW HW LJ 0.04450 2.77489
CW C LJ 0.10196 3.62284
CW O LJ 0.14419 3.21870
CW N LJ 0.12973 3.52491
OY OY LJ 0.17000 3.07000
OY HA LJ 0.07141 2.77038
OY HW LJ 0.07141 2.59885
OY C LJ 0.16363 3.39301
OY O LJ 0.23141 3.01450
OY N LJ 0.20821 3.30129
HA HA LJ 0.03000 2.50000
HA HW LJ 0.03000 2.34521
HA C LJ 0.06874 3.06186
HA O LJ 0.09721 2.72029
HA N LJ 0.08746 2.97909
HW HW LJ 0.03000 2.20000
HW C LJ 0.06874 2.87228
HW O LJ 0.09721 2.55186
HW N LJ 0.08746 2.79464
C C LJ 0.15750 3.75000
C O LJ 0.22274 3.33167
C N LJ 0.20041 3.64863
O O LJ 0.31500 2.96000
O N LJ 0.28342 3.24160
N N LJ 0.25500 3.55000
close

<pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh import *

reline = Fragment(coords="<name of pun file>.pun", connmode=None)
mm = DL_POLY(frag=reline, ff='name of ff file>.ff', temperature=0.0)

sp = SP(theory=mm)
sp.run()

#opt = Opt(theory=mm, maxcycle=100)
#opt.run()

<pre>

Mod:Hunt Research Group/Chemshell:Chemshell: MM Single Point computation inputs

2019-11-13T18:53:59Z

Dv4018: Created page with "Chose any name you like for the following files. The only thing that matters is the extension. The .pun file:"

Chose any name you like for the following files. The only thing that matters is the extension.

The .pun file:

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-07T15:20:58Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after loggig in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

...

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are asking ChemShell to compute the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and file we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:

# A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
# A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
# A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the function of the various commands it contains. In the following, please remember that ChemShell is written in Python language, After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise you're runscript will be useless.

Moving down we find:

reline = Fragment(coords="shell.pun", connmode=None)

Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode of the object; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:

mm = DL_POLY(frag=reline, ff='rel_wat_8.ff', temperature=0.0)

In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:

sp = SP(theory=mm)

Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

sp.run()

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

chemsh <module name>.py

At the end of the resulting output, you should get:

>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the old last two lines and uncomment the 'opt' lines. Save the canges to the script and run chemshell again with the same command as before:

chemsh <module name>.py

What changes in the output? Does the optimisation converges?

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-07T15:16:41Z

Dv4018:

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after loggig in to cx1:
<pre>
module load chemshell/ . . .
</pre>

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

...

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are asking ChemShell to compute the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and file we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:
- A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
- A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
- A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the function of the various commands it contains. In the following, please remember that ChemShell is written in Python language, After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise you're runscript will be useless.

Moving down we find:

reline = Fragment(coords="shell.pun", connmode=None)

Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode of the object; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:

mm = DL_POLY(frag=reline, ff='rel_wat_8.ff', temperature=0.0)

In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:

sp = SP(theory=mm)

Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

sp.run()

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

chemsh <module name>.py

At the end of the resulting output, you should get:

>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the old last two lines and uncomment the 'opt' lines. Save the canges to the script and run chemshell again with the same command as before:

chemsh <module name>.py

What changes in the output? Does the optimisation converges?

Mod:Hunt Research Group/Chemshell: MM Single Point computation

2019-11-07T15:14:56Z

Dv4018: Created page with "In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShe..."

In this tutorial we are going to start learning about the basic commands of ChemShell and the necessary inputs for QM/MM computations. First of all we need to load the ChemShell module after loggig in to cx1:

module load chemshell/ . . .

After that you need to create a new directory on the hpc home page and upload the input files there. All of the files you will need can be found here:

...

The first computation we are going to carry out with ChemShell is a simple MM (molecular mechanics) single point calculation. In other words we are asking ChemShell to compute the energy of a given atomic configuration, describing the interactions with the MM forcefield provided as one of the necessary inputs. The only output that will be generated is the energy of the configuration. Thus, this is neither a QM/MM computation nor an optimisation. Still, we will get to know the commands and file we will be using for all our QM/MM optimisations.

The files that you have just uploaded comprise:
- A .pun file, which contains the (initial) atomic positions (sorted by molecule type), and the charge carried by each atom.
- A .ff file, specifying the force field functional form and coefficients; the format of the .ff file will change accordingly to the package that we use for the MM computations: in our case we are using DL_POLY, therefore the .ff file will have exactly the same format of the DL_POLY FIELD input file.
- A .py file, this is the python module through which we specify the calculation that we want ChemShell to perform and define the value of all of the parameters involved.

Let's walk through the .py file to understand the function of the various commands it contains. In the following, please remember that ChemShell is written in Python language, After the commented title line, the first command imports all module contained in ChemShell. Remember always to include this line, otherwise you're runscript will be useless.

Moving down we find:

reline = Fragment(coords="shell.pun", connmode=None)

Here the new variable 'reline' is initialised as an object of the class 'Fragment'. Fragment objects are the ones containing the atomic position and charges, together with other info (connectivity, labels, ..). We will always need to define a Fragment object to run a computation in ChemShell, either as the starting configuration for an optimisation, or as the investigated configuration in a single point computation. The keyword argument 'coords'
defines the file from which to extract the atomic coordinates. The 'connmode' argument determines the connectivity mode of the object; for the moment you can ignore this command and always leave 'None' as the argument's value.

The next line in the .py script we find is:

mm = DL_POLY(frag=reline, ff='rel_wat_8.ff', temperature=0.0)

In this line we are defining the MM 'theory' for our calculation, i.e. the package, the forcefield, the initial configuration and all other relevant parameters for the MM part of the computation we want to perform. A number of optional keyword arguments is available for this object; let's focus on the required arguments for the moment.
The object class used in the definition, determines the package that will be used for the MM computations and consequently the accessible keyword arguments in the following definition. In our case we are going to use DL_POLY.
The 'frag' argument, determines which fragment object should be used as the starting point (in our case the only point) for our computation. Obviously, you need to define the fragment object of interest BEFORE using it as an argument in a definition/function. The subsequent argument 'ff' determines the file from which the forcefield will be imported for this computation. As already stated above, this file will need to have a suitable format depending on the package that we want to use for the MM computation. Finally, the 'temperature' argument trivially determines the temperature of the system during the computation. In most cases, you will be optimising a given structure neglecting any thermal movement (atomic kinetic energy = 0) and the assigned temperature value will be '0.0'

The last thing left to do before running, is to tell ChemShell the type of computation we want to perform. The next line in the .py script does just that:

sp = SP(theory=mm)

Here we initialise a new variable of a different object type depending on the required computation. In our case, we want to perform a Single Point Calculation, hence we use the object type SP(). SP object only have one necessary argument: 'theory'; with this argument we tell ChemShell the theory object from which to take all of the necessary information for the computation. We will talk about other optional keywords argument for this command later on.
Now we have all we need to perform a MM single point computation. The last line in the script:

sp.run()

is just telling ChemShell to run the computation defined within the 'sp' object.

Close the .py file and run this single point computation with the following command:

chemsh <module name>.py

At the end of the resulting output, you should get:

>>> Running single point calculation

>>> DL_POLY run successfully.
Peak memory used by procedure chemsh.base.run.run: 90.617 MB
Elapsed time of procedure chemsh.interfaces.mm.run: 0.168 sec

----------------------------------------------------------------------
Final SP energy = -0.195569750490 a.u.
----------------------------------------------------------------------

Elapsed time of procedure chemsh.tasks.sp.run: 0.169 sec

Now that we have successfully computed the MM energy of our initial configuration, let's run an MM optimisation!

To run an optimisation with the same MM 'theory' (same package, forcefield, initial configuration, temperature, ecc..) as the single point just performed we just need to modify the last two lines in the script, changing the computation type from SP (Single Point) to Opt (Optimisation). To make things even easier for you, the two new lines required are already reported at the end of the script, commented out. Just comment the old last two lines and uncomment the 'opt' lines. Save the canges to the script and run chemshell again with the same command as before:

chemsh <module name>.py

What changes in the output? Does the optimisation converges?