ChemWiki - User contributions [en]

Talk:Mod:Hunt Research Group/sdfs generate

2015-07-19T14:52:56Z

Rpmatthe: Created page with "Generating Spatial Distribution Functions using TRAVIS M. Brehm and B. Kirchner; J. Chem. Inf. Model. 2011, 51, 2007-2023 In general, spatial distribution functions (SDFs) m..."

Generating Spatial Distribution Functions using TRAVIS

M. Brehm and B. Kirchner; J. Chem. Inf. Model. 2011, 51, 2007-2023

In general, spatial distribution functions (SDFs) may be thought of as 3D enhancements to radial distribution functions (RDFs). Remember that RDFs indicate the probability of finding a particle/atom within a radially averaged distance to another particle/atom.

Thus, SDFs depict the probability of finding a ‘particle/atom’ at a particular position in space around a fixed reference system consisting of other particles/atoms.

To generate an SDF we must

Select a reference molecule. For example, we select the bmim cation as the reference molecule, provided we want to locate the average position of Cl anions relative to a bmim cation.

Moreover, to set up the reference frame, three atoms (which must not be located in one line) are chosen within the reference molecule. TRAVIS places the first atom at the origin, the second atom is located on the positive X axis, and the third atom is put into the X-Y plane (with positive Y value). This is done to allow for averaging of probabilities in the space around the reference molecule. More details can be obtained from the TRAVIS reference. Very Important: As 3 atoms are defined to setup a reference molecule no single ions (i.e. Cl-) can be used as a reference.

Select the atom/particle to observe using either INTRAMOLECULAR or INTERMOLECULAR

For example to select Cl relative to bmim

I recommend leaving selections including the RADIUS OF THE SDF and the BINNING RESOLUTION at the default values.

Two selections, degree of smoothing and the values at which the iso-surfaces are typically given i.e. the unit of particle density (nm-3 or pm-3), are important.

These are important as the SDF probability in 3-D space is a 4-D function, which is obviously hard to visualize as it is. It is necessary to reduce the dimensionality to three (or even lower). A common and reasonable method for doing so is to visualize iso-surfaces on the data, which can be easily drawn in three-dimensional space. Isosurfaces are surfaces that pass through all areas with the same probability. The values of iso-surfaces are typically given in the unit of particle density (nm-3 or pm-3), specifying the particle density along the iso-surface.

Moreover, when analysing short or medium size trajectories, the sampling of data is usually too poor for direct SDF creation. This results in poor SDFs, the appearance of which can be improved by smoothing the underlying data. More details can be found in the TRAVIS paper.the cations is observed.

I recommend using 3 smoothing degrees and either of the iso-value scales.

Visualising the SDF using VMD

1. Open VMD

2. Load the reference XYZ coordinates generated by TRAVIS as a NEW MOLECULE

Use FILE –– New Molecule

3. Load generated SDF .cube file for the reference coordinates. Make sure you are aware of the original and smoothed versions (include .sx.; i.e. original = name.cube, S1 = name.s1.cube, S3 = name.s3.cube).

4. Generate Graphical representations

Graphics –– Representations

5. I like to change the drawing method to CPK for the coordinates.

6. Create a representation for the isosurface.

Drawing method = Isosurface, Vol = the file you have loaded, Isovalue = what you require (NB 1 is bulk) – in the example I have used 2.5, which represents 2.5 times bulk (higher probability than average), Draw = Solid Surface, Show = Isosurface. Colouring method = whatever you want!!!

Mod:Hunt Research Group

2015-07-19T14:51:34Z

Rpmatthe: /* Visualisation */

==Hunt Group Wiki==

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

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
*'''MD Post processing'''
#Code to Recentre DL_PLOY HISTORY file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/recentre_xyz.py link]
#Link to the code to convert the DL_POLY HISTORY file to the multi-frame XYZ file[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/his2xyz.py link]

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

===Gaussian General===
#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]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Problems with Z-Matrix [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]

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

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#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]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

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

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

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

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

Mod:Hunt Research Group

2015-07-19T14:50:56Z

Rpmatthe: /* Visualisation */

==Hunt Group Wiki==

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

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
*'''MD Post processing'''
#Code to Recentre DL_PLOY HISTORY file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/recentre_xyz.py link]
#Link to the code to convert the DL_POLY HISTORY file to the multi-frame XYZ file[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/his2xyz.py link]

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

===Gaussian General===
#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]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Problems with Z-Matrix [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]

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

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#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]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

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

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

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

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

Mod:Hunt Research Group

2015-07-19T14:50:14Z

Rpmatthe: /* Visualisation */

==Hunt Group Wiki==

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

===Visualisation===
*'''density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]

*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD: a molecular dynamics visualisation package'''
#Download VMD [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/download_vmd link]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Tricks and tips [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDTips link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Basic visualisation of a trajectory [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding link]
#Atom selection and more advanced GUI based visualisation (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]
*'''PyGauss'''
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
*'''MD Post processing'''
#Code to Recentre DL_PLOY HISTORY file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/recentre_xyz.py link]
#Link to the code to convert the DL_POLY HISTORY file to the multi-frame XYZ file[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/his2xyz.py link]

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

===Gaussian General===
#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]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#Problems with Z-Matrix [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]

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

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#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]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

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

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

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

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

Mod:Hunt Research Group/calendar

2014-12-16T12:04:14Z

Rpmatthe:

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

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Done)
| Matthew Clough (Not Done)
| Bryan Ward (Done)
| Claire Ashworth (Done)
|-
| Precious Ugbomah (Done)
| Richard Matthews (Done)
| Vincent Chen (Done)
| Gabriel Lau (Not Done)
|-
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Ken Watson (Done)
| Laila Bana (Done)
|-
| Oliver Benton (Not Done)
|Christopher Sewell (Not Done)
|Chen Chen (Not Done)
|Aiswarya Prabha (Not Done)
|-
|-)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">'''1st December''' </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard F Away </td>
<td>9th Richard F Away </td>
<td>10th Richard F Away </td>
<td>11th Richard F Away </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Richard M Away </td>
<td>16th Richard F Away Richard M Away </td>
<td>17th Richard F Away Richard M Away </td>
<td>18th Richard M Away </td>
<td bgcolor="#FFFF00">19th '''END OF TERM''' Bryan Away Precious Away Richard M Away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Tricia Away Ken Away Bryan Away Precious Away Richard M Away Aiswarya Away </td>
<td>23rd Tricia Away Ken Away Claire Away Precious Away Richard M Away Aiswarya Away </td>
<td bgcolor="#33CC99">24th '''College closed'''</td>
<td bgcolor="#33CC99">25th '''College closed'''</td>
<td bgcolor="#33CC99">26th '''College closed'''</td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td bgcolor="#33CC99">29th '''College closed'''</td>
<td bgcolor="#33CC99">30th '''College closed'''</td>
<td bgcolor="#33CC99">31st '''College closed'''</td>
<td bgcolor="#4357CFF">'''1st January 2015''' '''College closed'''</td>
<td bgcolor="#33CC99">2nd '''College closed'''</td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<tr valign="top">
<td>5th Precious Away Aiswarya Away </td>
<td>6th Aiswarya Away </td>
<td>7th Aiswarya Away </td>
<td>8th Aiswarya Away </td>
<td>9th Aiswarya Away </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">12th '''NEW TERM''' Aiswarya Away (P) </td>
<td>13th Aiswarya Away (P) </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">'''1st February 2015''' </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-09-10T11:49:18Z

Rpmatthe:

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

{| class="wikitable"
|-
! 1
! 2
! 3
! 4
|-
| Tricia (Not Done)
| Abdihakim Hassan (Not Done)
| Bryan Ward (Not Done)
| Claire Ashworth (Not Done)

|-
| Matthew Clough (Done)
| Precious Ugbomah ( Done)
| Richard Matthews (Done)
| Vincent Chen (Not Done)
|-
| Gabriel Lau (Not Done)
| Rebecca Rowe (Not Done)
| Patricia Ho (Done)
| Giacomo Damilano (Not Done)
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td>28th Matthew Away jacq away </td>
<td>29th Matthew Away </td>
<td>30th Matthew Away </td>
<td>31st Bryan Away Matthew Away </td>
<td bgcolor="#4357CFF">1st August Bryan Away Matthew Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus Matthew Away </td>
<td>5th Bryan on hiatus Matthew Away </td>
<td>6th Bryan on hiatus Matthew Away </td>
<td>7th Bryan on hiatus Matthew Away Tricia ACS </td>
<td>8th Bryan on hiatus Matthew Away Tricia ACS </td>
<td bgcolor="#CCCCCC">9th Tricia ACS </td>
<td bgcolor="#CCCCCC">10th Tricia ACS </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus Matthew Away Tricia ACS Claire away</td>
<td>12th Bryan on hiatus Tricia ACS Richard F Away </td>
<td>13th Bryan on hiatus Tricia ACS Richard F Away </td>
<td>14th Bryan on hiatus Tricia ACS Richard F Away </td>
<td>15th Bryan on hiatus Tricia ACS Richard F Away </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus Tricia Holiday Richard F Away Precious Away </td>
<td>19th Bryan on hiatus Tricia Holiday Precious Away </td>
<td>20th Bryan on hiatus Tricia Holiday Precious Away </td>
<td>21st Bryan on hiatus Tricia Holiday Precious Away </td>
<td>22nd Bryan on hiatus Tricia Holiday Precious Away </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus Precious Away </td>
<td>27th Bryan on hiatus Precious Away </td>
<td>28th Bryan on hiatus Precious Away </td>
<td>29th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus Richard F Away </td>
<td>4th Bryan on hiatus Richard F Away </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th Tricia Holiday </td>
<td>12th Tricia Holiday </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Tricia Holiday Richard F Away </td>
<td>16th Tricia Holiday Richard F Away Richard M Away </td>
<td>17th Tricia Holiday Richard F Away Richard M Away </td>
<td>18th Tricia Holiday Richard F Away Richard M Away </td>
<td>19th Tricia Holiday Richard F Away Richard M Away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Tricia Holiday Richard F Away Richard M Away </td>
<td>23rd Tricia Holiday Richard F Away Richard M Away </td>
<td>24th Tricia Holiday Richard M Away </td>
<td>25th Tricia Holiday Richard M Away </td>
<td>26th Tricia Holiday Richard M Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th Tricia APCIL </td>
</tr>
<tr valign="top">
<td>29th Tricia APCIL </td>
<td>30th Tricia APCIL </td>
<td bgcolor="#4357CFF">1st October Tricia APCIL </td>
<td>2nd Tricia flying </td>
<td>3rd Tricia flying </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#FFFF00">6th '''NEW TERM''' </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
</table>

Talk:Mod:Hunt Research Group/Starting MD

2014-07-30T16:01:24Z

Rpmatthe:

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

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

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

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

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

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

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

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

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

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

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

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

Talk:Mod:Hunt Research Group/Starting MD

2014-07-30T16:00:54Z

Rpmatthe:

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

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

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

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

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

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

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

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

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

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

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

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

Talk:Mod:Hunt Research Group/Starting MD

2014-07-30T16:00:14Z

Rpmatthe: /* quick relaxation */

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

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

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

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

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

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

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

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

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

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

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

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

Mod:Hunt Research Group/conv xyz2conf

2014-07-30T15:46:02Z

Rpmatthe:

<code>#!/usr/bin/perl

$name=$ARGV[0];

$i=1;

open(PDB,"${name}.xyz");

while($line=<PDB>){

if($line=~/ NA /){

chomp($line);

@data=split(/ +/,$line);

$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];

$i++;

}

if($line=~/ CL /){

chomp($line);

@data=split(/ +/,$line);

$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];

$i++;

}

if($line=~/ OH2 /){

chomp($line);

@data=split(/ +/,$line);

$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];

$i++;

}

if($line=~/ HO /){

chomp($line);

@data=split(/ +/,$line);

$atomType[$i]=$data[1];$atomX[$i]=$data[2];$atomY[$i]=$data[3];$atomZ[$i]=$data[4];

$i++;

}

}

open(CFG,">${name}.cfg");

$header="Converted from Packmol XYZ\n";

print CFG $header;

printf CFG "%10d%10d%10d%20.6f\n",0,0,0,0;

printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;

printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;

printf CFG "%20.12f%20.12f%20.12f\n",0,0,0;

#writing atom types and coordinates into DL_POLY CONFIG

for($i=1;$i<=$#atomType;$i++){

printf CFG "%-8s%10d\n",$atomType[$i],$i;

printf CFG "%20.6f%20.6f%20.6f\n",$atomX[$i],$atomY[$i],$atomZ[$i];

}

close(CFG);
close(PDB);</code>

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-14T08:17:43Z

Rpmatthe:

When carrying out NPT and NVT simulations with Nose-Hover (Equilibration and Production) you may come across a drift in the Total Configuration Energy.
This may present itself with either a [[positive]] or [[negative]] slope.

This may occur for several reasons. '''(list to be expanded if and when more problems are encountered)'''

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=5 is shown

[[File:MD screenshot-CA.png]]

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL - with shake=1e-5

[[File:Screen-shot bmimcl-incorrect shake.png]]

and corrected with shake=1e-8

[[File:Screen-shot bmimcl 400K-corr.png]]

The second solution was obtained from the DL_POLY forum - '''http://www.cse.scitech.ac.uk/disco/forums/ubbthreads.php?ubb=showflat&Number=2881&page=1'''

Which points to the fact that using a lower shake tolerance leads to poor conservation of the total energy.

A concise reason for this is being formulated!!

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-14T08:16:11Z

Rpmatthe:

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-14T07:56:23Z

Rpmatthe:

When carrying out NPT and NVT simulations during the equilibration process you make come across a drift in the Total Configuration Energy.
This may present itself with either a [[positive]] or [[negative]] slope.

This may occur for several reasons. '''(list to be expanded if and when more problems are encountered)'''

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=5 is shown

[[File:MD screenshot-CA.png]]

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL - with shake=1e-5

[[File:Screen-shot bmimcl-incorrect shake.png]]

and corrected with shake=1e-8

[[File:Screen-shot bmimcl 400K-corr.png]]

The second solution was obtained from the DL_POLY forum - '''insert link here'''

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-12T12:15:49Z

Rpmatthe:

When carrying out NPT and NVT simulations during the equilibration process you make come across a drift in the Total Configuration Energy.
This may present itself with either a [[positive]] or [[negative]] slope.

This may occur for several reasons. '''(list to be expanded if and when more problems are encountered)'''

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

[[File:MD screenshot-CA.png]]

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL - with shake=1e-5

[[File:Screen-shot bmimcl-incorrect shake.png]]

and corrected with shake=1e-8

[[File:Screen-shot bmimcl 400K-corr.png]]

The second solution was obtained from the DL_POLY forum - '''insert link here'''

Paraphrase link...

File:MD screenshot-CA.png

2014-04-12T12:14:29Z

Rpmatthe:

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-11T16:24:50Z

Rpmatthe:

When carrying out NPT and NVT simulations during the equilibration process you make come across a drift in the Total Configuration Energy.
This may present itself with either a [[positive]] or [[negative]] slope.

This may occur for several reasons. '''(list to be expanded if and when more problems are encountered)'''

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL - with shake=1e-5

[[File:Screen-shot bmimcl-incorrect shake.png]]

and corrected with shake=1e-8

[[File:Screen-shot bmimcl 400K-corr.png]]

The second solution was obtained from the DL_POLY forum - '''insert link here'''

Paraphrase link...

File:Screen-shot bmimcl 400K-corr.png

2014-04-11T16:21:58Z

Rpmatthe:

File:Screen-shot bmimcl-incorrect shake.png

2014-04-11T16:19:33Z

Rpmatthe: Shake set at 1e-5 and not 1e-8 gives energy drift.

Shake set at 1e-5 and not 1e-8 gives energy drift.

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:09:13Z

Rpmatthe:

When carrying out NPT and NVT simulations during the equilibration process you make come across a drift in the Total Configuration Energy.
This may present itself with either a positive or negative slope as shown.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL -

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:07:58Z

Rpmatthe:

When carrying out NPT and NVT simulations during the equilibration process you make come across a drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL -

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:06:37Z

Rpmatthe:

When carrying out NPT and NVT simulations during equilibrations you make come across a drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL -

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:05:23Z

Rpmatthe:

When carrying out NPT and NVT simulations during equilibrations you make come across an drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)

2 examples are
1. Two atoms coming too close together and repelling each other strongly.
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to an energy drift.

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is illustrated below for an NVT simulation at 400K - [BMIM]CL -

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:04:13Z

Rpmatthe:

When carrying out NPT and NVT simulations during equilibrations you make come across an drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)
2 examples are

1. Two atoms coming too close together and repelling each other strongly
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to
an energy drift

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example for case 2 is shown below for an NVT simulation at 400K - [BMIM]CL -

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T22:02:57Z

Rpmatthe:

When carrying out NPT and NVT simulations during equilibrations you make come across an drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons. (list to be expanded if and when more problems are encountered)
2 examples are

1. Two atoms coming too close together and repelling each other strongly
2. Shake tolerance is not set to a sufficiently high level thus the constraints are not properly constrained leading to
an energy drift

To correct for 1. use capping and scale as recommended by Ruth for melting an IL from the crystal structure
:::*The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*Use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

An example of example 2 is shown for an [BMIM]CL NVT simulation at 400K

with shake set at 10-5

and shake=10-8

This solution was obtained from the DL_POLY forum - insert link here

Paraphrase link...

Talk:Mod:Hunt Research Group/EnergyDrift

2014-04-10T21:56:55Z

Rpmatthe: Created page with "When carrying out NPT and NVT simulations during equilibrations you make come across an drift in the Total Configuration Energy. This may have a positive or negative slope. An e..."

When carrying out NPT and NVT simulations during equilibrations you make come across an drift in the Total Configuration Energy.
This may have a positive or negative slope. An example is shown in the Figure below.

This may occur for several reasons such as
1. Two atoms coming too close together and repelling each other strongly

2. Shake tolerance is not set to a sufficiently high level.

To correct for 1 use capping and scale as recommended by Ruth for melting an IL from the crystal structure
::: The capping default=1000 but use 2000 kbT per Å (Ruth)
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces.
:::*use scaling, every 5 or 10 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

an example of the E-Tot plot using capping=1000 and scaling=10 is shown

::test with 100 steps, with scaling and capping of forces, and step ≈2fs
:::start from the above NVE relaxed structure
:::use nvt hoover 0.1, have checked that 0.1 and 0.5 give same result for temperature.
:::in case of [BMIM][BF4] or [BMIM][NO3], check that it ends at ~400K.
:::check that the pressure tensor is small ~E-01/-02.

::if start from grid, then melt the solid, in case of IL
:::*T=1000K for 20ps (20,000 steps)
:::*use capping, default=1000 but use 2000 kbT per Å
::::capping constrains the forces on individual atoms to be smaller or equal to a particular value and resets large forces to capping the capping value
:::*use scaling, every 5 steps
::::scaling scales all atomic velocities by the same amount to reproduce desired temperature (??)

::test with 100 steps, no scaling or capping of forces, and step ≈1fs, check that temp is not exploding
:::if there is a problem, we want to nudge system back to a good position, problem may well be two atoms coming too close together and repelling each other strongly
:::*shorten the time step 0.1fs
:::*add capping, default of 1000
:::another option maybe to use "zero" which resets target temp to 10K
::now we want to equilibrate at the desired temperature use NVT
:::*for IL this is probably around 400-500K
:::*total run is about 90-100ps
:::*run in batches of ≈30ps
:::*time step is 2fs (15,000 steps)
:::*capping, default=1000
:::*scaling, every 5 steps
:::*since this is all equilibration, set collect so data is collected

4. check for equilibration of temperature, from the same config file run multiple tests
::*run 30ps with no equilibration in NVT with thermostat (hoover 0.1 is working well, and hoover 0.1 or 0.5 give same temperature.)
:::looking for ±20K in T (checked - true)
:::look at the pressure, fluctuations can be large (size: pressure tensor ~E-01/-02), the smaller the box size the larger these fluctuations, we want pressure average of 1Atm ≈0kAtm (my final pressure 1.5Atm ≈0kAtm)
:::look at the pressure tensor, Pxx=Pyy=Pzz but there will be variations, size of these difference indicate accuracy, also off-diagonal terms should be zero again difference from zero indicates accuracy, looking for \"small\" differences
::*run 30ps with no constraints in NVE and look at the total energy, this should not drift (checked - no drift, conserved beautifully)
::*start several runs with different time step (eg 2fs and 1fs), if you double time step oscillations in E should increase (checked: true)

5. now we want to check the volume use NPT
::*we want to match volume to the experimental value
::*30ps, 2fs time step (15,000 steps) look to see the volume stabilising
:::find the volume by averaging over a WHOLE NPT run, as the last volume will be random
:::may need to manually increase or decrease box volume, use small steps!
:::if reducing volume must check that atoms do not get too close
:::if increasing volume must check that molecules remain together (use Ruth's script to rebuild molecules)
:::no capping or scaling
::*200ps production run
:::my density for [BMIM][BF4] at 300K 1.188 g cm-3 using Amber forcefield from Mario given by Ruth (compared to Liu06, at 300K UA 1.208, AA 1.194, EXP 1.211).

Mod:Hunt Research Group

2014-04-10T21:47:29Z

Rpmatthe:

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
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#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
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===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
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===Research Notes===
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#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]
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===Installing and using other packages===
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===Admin Stuff===
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Mod:Hunt Research Group/calendar

2014-03-28T09:32:34Z

Rpmatthe:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Matthew)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th '''(Tricia)'''</td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Richard away</td>
<td>24th Richard away</td>
<td>25th Richard away</td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM</td>
</tr>
<tr valign="top">
<td>7th EUCHEM</td>
<td>8th EUCHEM</td>
<td>9th EUCHEM</td>
<td>10th EUCHEM</td>
<td>11th EUCHEM</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-03-28T09:30:19Z

Rpmatthe:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)''' DL_Poly workshop - Claire, Richard</td>
<td>2nd DL_Poly workshop - Claire, Richard </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Matthew)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th '''(Tricia)'''</td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Richard away</td>
<td>24th Richard away</td>
<td>25th Richard away</td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th CECAM workshop</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away</td>
<td>15th Richard away</td>
<td>16th Richard away</td>
<td>17th Richard away</td>
<td>18th Richard away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd </td>
<td>23rd Gaussian workshop - Claire</td>
<td>24th Gaussian workshop - Claire</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>

<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-03-17T16:36:00Z

Rpmatthe:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st February Claire away</td>
<td bgcolor="#CCCCCC">2nd Claire away</td>
</tr>
<tr valign="top">
<td>3rd Claire away</td>
<td>4th '''(Hakim)''' Claire away</td>
<td>5th Claire away</td>
<td>6th Claire away</td>
<td>7th Claire away</td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th '''(Matthew)'''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Claire)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Richard)'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away Vincent away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Becky)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Giacomo)''' Richard postdoc workshop</td>
<td>19th </td>
<td>20th </td>
<td>21st Claire away</td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)'''</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Matthew)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th '''(Tricia)'''</td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th </td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th </td>
<td >20th </td>
<td>21st </td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</table>

Mod:Hunt Research Group/calendar

2014-01-20T10:11:46Z

Rpmatthe:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (NOt Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td > </td>
<td > </td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away Precious away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away Precious away Patricia away</td>
<td>7th Bryan Away Precious away Patricia away</td>
<td>8th Bryan Away Patricia away Precious away</td>
<td>9th Bryan Away Patricia away</td>
<td>10th Bryan Away Patricia away Claire-MSDG</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st '''(Bryan)''' Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away Claire away</td>
<td bgcolor="#CCCCCC">25th Claire away</td>
<td bgcolor="#CCCCCC">26th Claire away</td>
</tr>
<tr valign="top">
<td>27th Claire away</td>
<td>28th '''(Gabriel)''' Claire away</td>
<td>29th Claire away</td>
<td>30th Claire away</td>
<td>31st Claire away</td>
<td bgcolor="#4357CFF">1st February Claire away</td>
<td bgcolor="#CCCCCC">2nd Claire away</td>
</tr>
<tr valign="top">
<td>3rd Claire away</td>
<td>4th '''(Hakim)''' Claire away</td>
<td>5th Claire away</td>
<td>6th Claire away</td>
<td>7th Claire away</td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th '''(Matthew)'''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Richard)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Claire)'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Giacamo)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Becky)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)'''</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Tricia & DFT functionals)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th </td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>

</table>

Mod:Hunt Research Group/calendar

2014-01-20T10:11:15Z

Rpmatthe:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (NOt Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>

<tr valign="top">
<td > </td>
<td > </td>
<td bgcolor="#4357CFF">1st January '''College closed'''</td>
<td>2nd Richard away Claire away Tricia away Giacomo Away Patricia away Precious away</td>
<td>3rd Richard away Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">4th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
<td bgcolor="#CCCCCC">5th Gabriel & Vincent - Science Communication Course Bryan Away Tricia away Giacomo Away Patricia away Precious away</td>
</tr>
<tr valign="top">
<td>6th Bryan Away Precious away Patricia away</td>
<td>7th Bryan Away Precious away Patricia away</td>
<td>8th Bryan Away Patricia away Precious away</td>
<td>9th Bryan Away Patricia away</td>
<td>10th Bryan Away Patricia away Claire-MSDG</td>
<td bgcolor="#FFA500">11th '''Start of term'''</td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th Vincent Away</td>
<td>14th Vincent Away</td>
<td>15th Vincent Away</td>
<td>16th Vincent Away</td>
<td>17th Vincent Away</td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th Vincent Away</td>
<td>21st '''(Bryan)''' Vincent Away</td>
<td>22nd Vincent Away</td>
<td>23rd Vincent Away</td>
<td>24th Vincent Away Claire away</td>
<td bgcolor="#CCCCCC">25th Claire away</td>
<td bgcolor="#CCCCCC">26th Claire away</td>
</tr>
<tr valign="top">
<td>27th Claire away</td>
<td>28th '''(Gabriel)''' Claire away</td>
<td>29th Claire away</td>
<td>30th Claire away</td>
<td>31st Claire away</td>
<td bgcolor="#4357CFF">1st February Claire away</td>
<td bgcolor="#CCCCCC">2nd Claire away</td>
</tr>
<tr valign="top">
<td>3rd Claire away</td>
<td>4th '''(Hakim)''' Claire away</td>
<td>5th Claire away</td>
<td>6th Claire away</td>
<td>7th Claire away</td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th </td>
<td>11th '''(Matthew)'''</td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Richard)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Claire)'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>
<tr valign="top">
<td>3rd Richard away </td>
<td>4th '''(Vincent)''' Richard away </td>
<td>5th Richard away </td>
<td>6th Richard away </td>
<td>7th Richard away </td>
<td bgcolor="#CCCCCC">8th </td>
<td bgcolor="#CCCCCC">9th </td>
</tr>
<tr valign="top">
<td>10th Richard away </td>
<td>11th '''(Giacamo)''' Richard away </td>
<td>12th Richard away </td>
<td>13th Richard away </td>
<td>14th Richard away </td>
<td bgcolor="#CCCCCC">15th </td>
<td bgcolor="#CCCCCC">16th </td>
</tr>
<tr valign="top">
<td>17th </td>
<td>18th '''(Becky)'''</td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#CCCCCC">22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
</tr>
<tr valign="top">
<td>24th </td>
<td>25th '''(Patricia)'''</td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''End of term'''</td>
<td bgcolor="#CCCCCC">29th </td>
<td bgcolor="#CCCCCC">30th </td>
</tr>
<tr valign="top">
<td>31st </td>
<td bgcolor="#4357CFF">1st April '''(Precious)'''</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
<tr valign="top">
<td>7th </td>
<td >8th '''(Tricia & DFT functionals)'''</td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th </td>
<td >15th </td>
<td>16th </td>
<td bgcolor="#339933">17th '''College Closed'''</td>
<td bgcolor="#339933">18th '''College Closed'''</td>
<td bgcolor="#CCCCCC">19th '''College Closed'''</td>
<td bgcolor="#CCCCCC">20th '''College Closed'''</td>
</tr>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td bgcolor="#FFA500">26th '''Start of term'''</td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td >29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th </td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>

</table>

Mod:Hunt Research Group/calendar

2013-11-20T13:19:31Z

Rpmatthe:

Mod:Hunt Research Group/calendar

2013-11-20T13:17:54Z

Rpmatthe:

Mod:Hunt Research Group/calendar

2013-11-20T13:17:08Z

Rpmatthe:

Mod:Hunt Research Group

2013-09-26T15:45:23Z

Rpmatthe: /* Gaussian General */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#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]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

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

===Setup and Running Classical MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#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]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

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

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/calendar

2013-08-28T15:28:45Z

Rpmatthe:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| <s>Matrix Mechanics</s> ||Gabriel|| <s>1st August</s>
|-
| 4 || Linear Algebra || Richard || Postponed
|-
| 5 || Chem. I - topic TBD ||Bryan || 5th September
|-
| 6 ||Perturbation Theory|| Vincent|| 19th September
|-
| 7 ||Chem. II - topic TBD || Precious || 3rd October
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard Away Sarah Away Precious Away Bryan Away </td>
<td>9th '''(Vincent)''' Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>10th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>11th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>12th Richard Away Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th '''(Gabriel)''' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Matthew Away Precious Away </td>
<td>19th Matthew Away Precious away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd '''(Sarah)'''</td>
<td>24th </td>
<td>25th </td>
<td>26th Matthew Away Gabriel Away Bryan Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th Matthew Away Gabriel Away </td>
<td>30th '''(Tricia)''' Gabriel Away </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August '''Theory Meeting'''</td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Bryan Away Matthew/Claire-GSC-6 working from home Precious</td>
<td>8th Tricia away Vincent Away Bryan Away</td>
<td>9th Tricia away Vincent Away Bryan Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away Matthew Away Bryan Away Claire Away</td>
<td>13th Tricia away Vincent Away Matthew Away Bryan Away Claire Away</td>
<td>14th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>15th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td>16th Tricia away Vincent Away Matthew Away Bryan Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away Bryan Away</td>
<td>20th Vincent Away '''(Carlos)'''</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th '''(Richard)'''</td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
<tr valign="top">
<td>2nd Tricia -CPMD 2013</td>
<td>3rd Tricia -CPMD 2013 '''(Hakim)'''</td>
<td>4th Tricia -CPMD 2013</td>
<td>5th '''Theory Meeting''' Tricia -CPMD 2013</td>
<td>6th Tricia -CPMD 2013</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th Tricia away </td>
<td>10th Tricia away '''(Bryn)'''</td>
<td>11th Tricia away </td>
<td>12th Tricia away </td>
<td>13th Tricia away </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(Claire)'''</td>
<td>18th </td>
<td>19th '''Theory Meeting''' </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th '''(Precious)'''</td>
<td>25th </td>
<td>26th </td>
<td>27th Claire away</td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF">1st October '''(Matthew)'''</td>
<td>2nd </td>
<td>3rd '''Theory Meeting''' </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-07-05T15:49:34Z

Rpmatthe:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| Matrix Mechanics ||Gabriel|| 11th July
|-
| 4 || Linear Algebra || Richard || 25th July
|-
| 5 || Perturbation Theory ||Precious & Bryan || 8th August
|-
| 6 ||Fourier and Laplace Transformations || Vincent || TBD
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Richard Away Sarah Away Precious Away Bryan Away </td>
<td>9th '''(Vincent)''' Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>10th Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>11th '''Theory Meeting''' Richard Away Sarah Away Matthew Away MSDG Precious Away </td>
<td>12th Richard Away Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th '''(Sarah)''' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Matthew Away Precious Away </td>
<td>19th Matthew Away Precious away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd '''(Gabriel)'''</td>
<td>24th </td>
<td>25th '''Theory Meeting''' </td>
<td>26th Matthew Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th Matthew Away </td>
<td>30th '''(Tricia)'''</td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>8th '''Theory Meeting''' Tricia away Vincent Away</td>
<td>9th Tricia away Vincent Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away Matthew Away </td>
<td>13th Tricia away Vincent Away Matthew Away</td>
<td>14th Tricia away Vincent Away Matthew Away</td>
<td>15th Tricia away Vincent Away Matthew Away</td>
<td>16th Tricia away Vincent Away Matthew Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away </td>
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
<tr valign="top">
<td>2nd Tricia -CPMD 2013</td>
<td>3rd Tricia -CPMD 2013</td>
<td>4th Tricia -CPMD 2013</td>
<td>5th '''Theory Meeting''' Tricia -CPMD 2013</td>
<td>6th Tricia -CPMD 2013</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th '''Theory Meeting''' </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td>2nd </td>
<td>3rd '''Theory Meeting''' </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-07-05T12:03:26Z

Rpmatthe:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Theory Group Meetings: 2-3.30pm every other Thursday
!Meeting !! Topic || Name || Date
|-
| <s>1</s> || <s>Differentiation and Integration</s> || Matthew || <s>20th June</s>
|-
| <s>2</s> || <s>Differential Equations</s> || Claire || <s>27th</s> <s>June</s>
|-
| 3|| Matrix Mechanics ||Gabriel|| 11th July
|-
| 4 || Linear Algebra || Richard || 25th July
|-
| 5 || Perturbation Theory ||Precious & Bryan || 8th August
|-
| 6 ||Fourier and Laplace Transformations || Vincent || TBD
|}

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st July </td>
<td>2nd '''PhD Symposium '''</td>
<td>3rd </td>
<td>4th </td>
<td>5th Bryan Away ChemShell Workshop 10am-4pm</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th Sarah Away Precious Away Bryan Away </td>
<td>9th '''(Vincent)''' Sarah Away Matthew Away MSDG Precious Away </td>
<td>10th Sarah Away Matthew Away MSDG Precious Away </td>
<td>11th '''Theory Meeting''' Sarah Away Matthew Away MSDG Precious Away </td>
<td>12th Sarah Away Precious Away </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Precious Away </td>
<td>16th '''(Sarah)''' Precious Away </td>
<td>17th Precious Away </td>
<td>18th Matthew Away Precious Away </td>
<td>19th Matthew Away Precious away </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd '''(Gabriel)'''</td>
<td>24th </td>
<td>25th '''Theory Meeting''' </td>
<td>26th Matthew Away </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th Matthew Away </td>
<td>30th '''(Tricia)'''</td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th Matthew/Claire-GSC-6</td>
</tr>
<tr valign="top">
<td>5th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>6th Tricia away Vincent Away Matthew/Claire-GSC-6 </td>
<td>7th Tricia away Vincent Away Matthew/Claire-GSC-6</td>
<td>8th '''Theory Meeting''' Tricia away Vincent Away</td>
<td>9th Tricia away Vincent Away</td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td>12th Tricia away Vincent Away Matthew Away </td>
<td>13th Tricia away Vincent Away Matthew Away</td>
<td>14th Tricia away Vincent Away Matthew Away</td>
<td>15th Tricia away Vincent Away Matthew Away</td>
<td>16th Tricia away Vincent Away Matthew Away</td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td>19th Vincent Away </td>
<td>20th Vincent Away</td>
<td>21st Vincent Away</td>
<td>22nd '''Theory Meeting''' Vincent Away</td>
<td>23rd Vincent Away</td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">26th College Closed '''Bank Holiday'''</td>
<td>27th </td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st September </td>
</tr>
<tr valign="top">
<td>2nd Tricia -CPMD 2013</td>
<td>3rd Tricia -CPMD 2013</td>
<td>4th Tricia -CPMD 2013</td>
<td>5th '''Theory Meeting''' Tricia -CPMD 2013</td>
<td>6th Tricia -CPMD 2013</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th '''Theory Meeting''' </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td>27th </td>
<td bgcolor="#FFA500">28th '''Start of Term'''</td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td>2nd </td>
<td>3rd '''Theory Meeting''' </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2013-03-25T14:58:40Z

Rpmatthe:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Dimitrios Katsikadakos (Not Done)
*Ling Ge (Not Done)
*Precious Ugbomah (Done)
*Richard Matthews (Done)
*Vincent Chen (Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Group Meetings: Tuesday 3pm
! Week !! Meeting
|-
| 1 || Theory
|-
| 2 || Ionic Liquids: Structure and Reactivity
|-
| 3|| Rio Tinto (Chemistry)
|-
| 4 || Catalysis and Water
|-
| (5) || CAKE TIME! (i.e. social)
|}

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th Matthew Away </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)''</td>
<td>20th Claire working from home</td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th ''(Cat.+H2O)'' </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)'' </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th ''(Cat.+H2O)'' Precious away </td>
<td>27th Precious, Tricia away </td>
<td bgcolor="#2E8B57">28th College Closed Precious away on a course, Tricia in but not available, Richard working at home</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday''' Holiday</td>
<td bgcolor="#2E8B57">30th College Closed Holiday</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday''' Holiday</td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday''' Precious away Claire away </td>
<td bgcolor="#2E8B57">2nd College Closed Bryan, Precious, Claire away Richard, Tricia work from home</td>
<td>3rd Precious, Tricia working from home Richard, Claire away</td>
<td>4th Claire, Tricia work from home</td>
<td>5th Claire working at home Tricia will be in!</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>

<tr valign="top">
<td>8th </td>
<td>9th ''(ILs)''</td>
<td>10th </td>
<td>11th </td>
<td>12th 6 month progress report '''deadline''' (Blackboard) </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Vincent away </td>
<td>16th ''(Rio)'' Vincent away</td>
<td>17th Vincent away</td>
<td>18th Vincent away</td>
<td>19th Vincent away</td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Vincent away</td>
<td>23rd ''(Cat.+H2O)'' Vincent away</td>
<td>24th Vincent away</td>
<td>25th Vincent away </td>
<td>26th Vincent away</td>
<td bgcolor="#FFCCFF">27th Start of Summer Term</td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th ''(CAKE)''</td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6th College Closed '''Bank Holiday'''</td>
<td>7th ''(Theory)''</td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th ''(ILs)''</td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st ''(Rio)''</td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">27th College Closed '''Bank Holiday'''</td>
<td>28th ''(Cat.+H2O)''</td>
<td>29th </td>
<td>30th </td>
<td>31st 2nd Yr PhD Students: '''deadline''' for submission of draft poster to Blackboard</td>
<td bgcolor="#4357CFF">1st June </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>

</table>

Mod:Hunt Research Group/calendar

2013-03-25T14:58:08Z

Rpmatthe:

== Calendar ==

*Tricia (Done)
*Abdihakim Hassan (Done)
*Bryan Ward (Done)
*Claire Ashworth (Done)
*Matthew Clough (Not Done)
*Dimitrios Katsikadakos (Not Done)
*Ling Ge (Not Done)
*Precious Ugbomah (Done)
*Richard Matthews (Not Done)
*Vincent Chen (Done)
*Gabriel Lau (Not Done)
*Sarah Smith (Not Done)

{| class="wikitable" border="1" style="text-align:center"
|+ Group Meetings: Tuesday 3pm
! Week !! Meeting
|-
| 1 || Theory
|-
| 2 || Ionic Liquids: Structure and Reactivity
|-
| 3|| Rio Tinto (Chemistry)
|-
| 4 || Catalysis and Water
|-
| (5) || CAKE TIME! (i.e. social)
|}

 
<table border="1" cellpadding="5">
<tr bgcolor="#66CCFF">
<th width="115px">Mon</th>
<th width="115px">Tues</th>
<th width="115px">Wed</th>
<th width="115px">Thur</th>
<th width="115px">Fri</th>
<th width="115px" bgcolor="#CCCCCC">Sat</th>
<th width="115px" bgcolor="#CCCCCC">Sun</th>
</tr>
<tr valign="top">
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td bgcolor="#4357CFF">1st February Claire Away</td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th Matthew Away </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)''</td>
<td>20th Claire working from home</td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td>25th </td>
<td>26th ''(Cat.+H2O)'' </td>
<td>27th </td>
<td>28th </td>
<td bgcolor="#4357CFF">1st March </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td >4th </td>
<td>5th ''(Theory)'' </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th ''(ILs)'' </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th ''(Rio)'' </td>
<td>20th </td>
<td>21st </td>
<td bgcolor="#FFCCFF">22nd End of Spring Term</td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td> 25th</td>
<td>26th ''(Cat.+H2O)'' Precious away </td>
<td>27th Precious, Tricia away </td>
<td bgcolor="#2E8B57">28th College Closed Precious away on a course, Tricia in but not available, Richard working at home</td>
<td bgcolor="#2E8B57">29th College Closed '''Good Friday''' Holiday</td>
<td bgcolor="#2E8B57">30th College Closed Holiday</td>
<td bgcolor="#2E8B57">31st College Closed '''Easter Sunday''' Holiday</td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st April College Closed '''Easter Monday''' Precious away Claire away </td>
<td bgcolor="#2E8B57">2nd College Closed Bryan, Precious, Claire away Richard, Tricia work from home</td>
<td>3rd Precious, Tricia working from home Richard, Claire away</td>
<td>4th Claire, Tricia work from home</td>
<td>5th Claire working at home Tricia will be in!</td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>

<tr valign="top">
<td>8th </td>
<td>9th ''(ILs)''</td>
<td>10th </td>
<td>11th </td>
<td>12th 6 month progress report '''deadline''' (Blackboard) </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th Vincent away </td>
<td>16th ''(Rio)'' Vincent away</td>
<td>17th Vincent away</td>
<td>18th Vincent away</td>
<td>19th Vincent away</td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd Vincent away</td>
<td>23rd ''(Cat.+H2O)'' Vincent away</td>
<td>24th Vincent away</td>
<td>25th Vincent away </td>
<td>26th Vincent away</td>
<td bgcolor="#FFCCFF">27th Start of Summer Term</td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th ''(CAKE)''</td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td>3rd </td>
<td bgcolor="#CCCCCC">4th </td>
<td bgcolor="#CCCCCC">5th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">6th College Closed '''Bank Holiday'''</td>
<td>7th ''(Theory)''</td>
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td bgcolor="#CCCCCC">11th </td>
<td bgcolor="#CCCCCC">12th </td>
</tr>
<tr valign="top">
<td>13th </td>
<td>14th ''(ILs)''</td>
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td bgcolor="#CCCCCC">18th </td>
<td bgcolor="#CCCCCC">19th </td>
</tr>
<tr valign="top">
<td>20th </td>
<td>21st ''(Rio)''</td>
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td bgcolor="#CCCCCC">25th </td>
<td bgcolor="#CCCCCC">26th </td>
</tr>
<tr valign="top">
<td bgcolor="#2E8B57">27th College Closed '''Bank Holiday'''</td>
<td>28th ''(Cat.+H2O)''</td>
<td>29th </td>
<td>30th </td>
<td>31st 2nd Yr PhD Students: '''deadline''' for submission of draft poster to Blackboard</td>
<td bgcolor="#4357CFF">1st June </td>
<td bgcolor="#CCCCCC">2nd </td>
</tr>

</table>

Talk:Mod:Hunt Research Group/EquilibrationandProduction

2013-02-20T14:57:01Z

Rpmatthe: Created page with "This needs to be setup correctly!!! 2. run NPT -don't want the dynamic properties here because of the forces applied to keep the pressure constant, these directly effect the dy..."

This needs to be setup correctly!!!

2. run NPT

-don't want the dynamic properties here because of the forces applied to keep the pressure constant, these directly effect the dynamic properties, use the NVT for properties.

starting from a roughly pre-equilibrated trajectory (NPT done)
this is your NVT simulation

-NVE is possible, but NVT conserves the temp and will correspond to experimental const temp
timestep given in ps, step size 1fs is standard (with H's)
a good equilibration for pure water is 200-500ps
but for ions in water, or ILs you need 2000-5000ps

want to check the temperature, total energy and maybe pressure
the temperature should oscillate +/- 5-10K around the set target value
the total energy should be conserved, you should see no drift after initial equilibration
the pressure can fluctuate widely

it is possible for a state to be reached where the temp increases continuously, or the energy fails to level off and decreases continuously this is bad. You will have errors in your input.

you can eyeball the numbers but it is best to visualise these
you can visualise using the dlpoly gui (part of the dlpoly source-code)
to use this on the cluster exporting your display you need to
login with -X option eg ssh -X username:hpc_path
then load the gui, type
<pre> > module load dl_poly/2.19 (return)
> gui (return)</pre>

now to visualise the temp and E

goto ANALYSIS

choose TEMP

then RUN

Talk:Mod:Hunt Research Group/VisualisingyourSimulation

2013-02-20T14:55:57Z

Rpmatthe: Created page with "After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory. 1. Confirm your production run is actually equilib..."

After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory.

1. Confirm your production run is actually equilibrated (same as what you did for the equilibration phase using CCP1GUI).

2. To visualise the atoms moving use VMD

http://www.ks.uiuc.edu/Research/vmd/

(follow their setup instructions)

transfer the HISTORY file to your local computer

FILE:NEW MOLECULE

BROWSE and choose the HISTORY file

select DLPOLY V2 as the file format

LOAD

if your file loads with bonds stretching across the screen

select GRAPHICS

under Drawing Method choose DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

check that your box has not exploded, a few molecules outside is ok, but not an increasing number of molecules, also it should be cube like and not deformed
if the box does deform you may have a box dimension too large/small and you should go back and complete a npt equilibration.

time guesstimates

for 4000 atoms,1ns=1000ps per day on 8proc

Talk:Mod:Hunt Research Group/Ensembles

2013-02-20T12:30:51Z

Rpmatthe:

This needs to be setup correctly.

Talk through the ensembles. Main ones needed are NVE, NVT and NPT.

Mod:Hunt Research Group

2013-02-20T12:30:02Z

Rpmatthe: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]

===Research Notes===
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/Visualising

2013-02-20T12:27:44Z

Rpmatthe:

After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory.

1. Confirm your production run is actually equilibrated (same as what you did for the equilibration phase using CCP1GUI).

2. To visualise the atoms moving use VMD

http://www.ks.uiuc.edu/Research/vmd/

(follow their setup instructions)

transfer the HISTORY file to your local computer

FILE:NEW MOLECULE

BROWSE and choose the HISTORY file

select DLPOLY V2 as the file format

LOAD

if your file loads with bonds stretching across the screen

select GRAPHICS

under Drawing Method choose DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

check that your box has not exploded, a few molecules outside is ok, but not an increasing number of molecules, also it should be cube like and not deformed
if the box does deform you may have a box dimension too large/small and you should go back and complete a npt equilibration.

time guesstimates

for 4000 atoms,1ns=1000ps per day on 8proc

Talk:Mod:Hunt Research Group/Equilibraton

2013-02-20T12:26:41Z

Rpmatthe:

Mod:Hunt Research Group

2013-02-20T12:25:29Z

Rpmatthe: /* Setup and Running MD Simulations */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Resources===

#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link] (notes by Tricia)

===Gaussian General===
#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] (notes by Everyone!)
#Instructions for visualizing electrostatic potentials [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link] (notes by Flo)
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#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] (notes by Heiko)
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link] (notes by Richard)
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link] (notes by Bryan & Richard)

===Unix and HPC===
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link] (notes by Hieu)
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link] (notes by Heiko)
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link] (notes by Tricia and Ling)]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link] (notes by Heiko)
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link] (notes by Heiko)
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link] (notes by Heiko)
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link] (notes by Heiko)
#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] (notes by Rachael and Weihong)
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link] (notes by Ling)

===Installing and using packages===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link] (notes by Ling)
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling & Bryan)
#DLPOLY a MD simulation package, Installation on an IMac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link] (notes by Ling)
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link] (notes by Tricia)
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link] (notes by Tricia)
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/] (Ling)
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link] (notes by Bryan)

===Setup and Running MD Simulations===
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link] (notes by Richard)
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link] (notes by Richard)
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Equilibraton link] (notes by Richard)
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Visualising link] (notes by Richard)
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link] (notes by Ling)
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link] (notes by Tricia and Ling)]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link] (notes by Ling)]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link] (notes by Ling and Tricia)]

===Research Notes===
#Cl- in water[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link] (notes by Ling)]
#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] (notes by Yannis)
#Functional for ILs using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link] (notes by Ling)
#[bmim]Cl using CPMD[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link] (notes by Ling)
#[bmim]Cl using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link] (notes by Ling)
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link] (notes by Ling)
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link] (notes by Ling)
#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] (notes by Ling)
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link] (notes by Ling)
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link] (notes by Ling)
#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)

===CDT records===
#Activities record [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/CDT_records records]

===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] (notes by Tricia)
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link] (notes by Tricia)
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar] (notes by Tricia)
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable] (notes by Tricia)
#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] notes by Tricia

Talk:Mod:Hunt Research Group/Visualising

2013-02-20T12:24:36Z

Rpmatthe:

After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory.
1. Confirm your production run is actually equilibrated (same as what you did for the equilibration phase).

1. setup

2. run NPT

-don't want the dynamic properties here because of the forces applied to keep the pressure constant, these directly effect the dynamic properties, use the NVT for properties.

starting from a roughly pre-equilibrated trajectory (NPT done)
this is your NVT simulation

-NVE is possible, but NVT conserves the temp and will correspond to experimental const temp
timestep given in ps, step size 1fs is standard (with H's)
a good equilibration for pure water is 200-500ps
but for ions in water, or ILs you need 2000-5000ps

want to check the temperature, total energy and maybe pressure
the temperature should oscillate +/- 5-10K around the set target value
the total energy should be conserved, you should see no drift after initial equilibration
the pressure can fluctuate widely

it is possible for a state to be reached where the temp increases continuously, or the energy fails to level off and decreases continuously this is bad. You will have errors in your input.

you can eyeball the numbers but it is best to visualise these
you can visualise using the dlpoly gui (part of the dlpoly source-code)
to use this on the cluster exporting your display you need to
login with -X option eg ssh -X username:hpc_path
then load the gui, type
<pre> > module load dl_poly/2.19 (return)
> gui (return)</pre>

now to visualise the temp and E

goto ANALYSIS

choose TEMP

then RUN

to visualise the atoms moving use VMD

http://www.ks.uiuc.edu/Research/vmd/

(follow their setup instructions)

transfer the HISTORY file to your local computer

FILE:NEW MOLECULE

BROWSE and choose the HISTORY file

select DLPOLY V2 as the file format

LOAD

if your file loads with bonds stretching across the screen

select GRAPHICS

under Drawing Method choose DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

check that your box has not exploded, a few molecules outside is ok, but not an increasing number of molecules, also it should be cube like and not deformed
if the box does deform you may have a box dimension too large/small and you should go back and complete a npt equilibration.

time guesstimates

for 4000 atoms,1ns=1000ps per day on 8proc

Talk:Mod:Hunt Research Group/Visualising

2013-02-20T12:22:25Z

Rpmatthe:

After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory.

First we want to confirm that the system is equilibrated.

1. setup

2. run NPT

-don't want the dynamic properties here because of the forces applied to keep the pressure constant, these directly effect the dynamic properties, use the NVT for properties.

starting from a roughly pre-equilibrated trajectory (NPT done)
this is your NVT simulation

-NVE is possible, but NVT conserves the temp and will correspond to experimental const temp
timestep given in ps, step size 1fs is standard (with H's)
a good equilibration for pure water is 200-500ps
but for ions in water, or ILs you need 2000-5000ps

want to check the temperature, total energy and maybe pressure
the temperature should oscillate +/- 5-10K around the set target value
the total energy should be conserved, you should see no drift after initial equilibration
the pressure can fluctuate widely

it is possible for a state to be reached where the temp increases continuously, or the energy fails to level off and decreases continuously this is bad. You will have errors in your input.

you can eyeball the numbers but it is best to visualise these
you can visualise using the dlpoly gui (part of the dlpoly source-code)
to use this on the cluster exporting your display you need to
login with -X option eg ssh -X username:hpc_path
then load the gui, type
<pre> > module load dl_poly/2.19 (return)
> gui (return)</pre>

now to visualise the temp and E

goto ANALYSIS

choose TEMP

then RUN

to visualise the atoms moving use VMD

http://www.ks.uiuc.edu/Research/vmd/

(follow their setup instructions)

transfer the HISTORY file to your local computer

FILE:NEW MOLECULE

BROWSE and choose the HISTORY file

select DLPOLY V2 as the file format

LOAD

if your file loads with bonds stretching across the screen

select GRAPHICS

under Drawing Method choose DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

check that your box has not exploded, a few molecules outside is ok, but not an increasing number of molecules, also it should be cube like and not deformed
if the box does deform you may have a box dimension too large/small and you should go back and complete a npt equilibration.

time guesstimates

for 4000 atoms,1ns=1000ps per day on 8proc

Talk:Mod:Hunt Research Group/Ensembles

2013-02-20T12:21:08Z

Rpmatthe:

This needs to be setup correctly.
2. run NPT

-don't want the dynamic properties here because of the forces applied to keep the pressure constant, these directly effect the dynamic properties, use the NVT for properties.

starting from a roughly pre-equilibrated trajectory (NPT done)
this is your NVT simulation

-NVE is possible, but NVT conserves the temp and will correspond to experimental const temp
timestep given in ps, step size 1fs is standard (with H's)
a good equilibration for pure water is 200-500ps
but for ions in water, or ILs you need 2000-5000ps