Mod:Hunt Research Group

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Hunt Group Wiki

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Report and Paper Writing

  1. procedures link
  2. advice link
  3. report components link
  4. files to provide when writing a paper link

Group Admin

  1. Which files to store on the database and database template link
  2. How to access DROBO link

HPC Resources

  1. Hunt group HPC servers and run scripts link
  2. How to use gaussview directly on the HPC link
  3. How to run jobs interactively link
  4. Computing resources available in the chemistry department link
  5. New gf script (more convenient job submitting) link
  6. Retired: How to make qsub more comfortable (gfunc) link
  7. Tired of entering your password all the time: set up a SSH keypair link
  8. How to make ssh more comfortable link
  9. How to comfortably search through old BASH commands link
  10. Using VPN from home, for Sierra follow the college instructions link
  11. How to connect to HPC directory on desktop for file transfers link
  12. How to set-up remote desktop link
  13. How to use a slimmed down terminal on your IPhone [1]

Using evil Windows and PCs

  1. Use Imperial Software Hub to access gaussview and gaussian link
  2. Using windows and setting up a connection to HPC link
  3. How to fix Windows files under UNIX link

Key Papers, References and Resources

  • Papers
  1. Meta study on DFT functionals doi
  2. M06 suite of DFT functionals doi
  3. SMD for ILs doi
  • Notes
  1. Solving the angular part of the Schrödinger equation for a hydrogen atom link (notes by Vincent)
  2. DFT Workshop Notes [2]
  3. Cl- in water link
  4. The use of Legendre time correlation functions to study reorientational dynamics in liquids link

Gaussian General

  1. We are starting a database of common errors encountered when running Gaussian jobs link
  2. Here is an already existing database of common errors link
  3. G03 Manual
  4. partial optimisations and scans link
  5. General procedure for locating transition state structures link
  6. How to include dispersion link
  7. Basic ONIOM (Mechanical Embedding) link
  8. IL ONIOM clusters link
  9. problems with scf convergence link
  10. manipulating checkpoint files link
  11. for NMR calculations look here: Chemical Shift Repository

Gaussian Advanced

  1. Systematic conformational scan for ion-pair dimers link
  2. How to run NBO5.9 on the HPC link
  3. generating natural transition orbitals link
  4. computing excited state polarisabilities link
  5. computing deuterated and/or anharmonic spectra link
  6. How to run at a higher temperature link
  7. Correcting the entropy due to low modes link
  8. Optimisation of charged molecules in an electric field link

Solvation

  1. Using solvent models link
  2. Using SMD on ILs link
  3. Troublesome optimisations in SMD link
  4. Atomic radii and solvent models link
  5. Molecular volume calculations link
  6. The cavity link
  7. How to download and use GeomView to visualise solvation cavities link
  8. Surfaces (Solvent-Accessible and Connolly) in Jmol link

Codes to Help Gaussian Analysis

  1. Extract last Standard Orientation structure of gaussian log file link
  2. Extract geometry and charges (ESP) into a .pdb file for visualising in VMD link
  3. Codes to extract CHELPG and NBO charge values to excel link
  4. Extract ESP and NBO charges link
  5. Extract E2 Values (From NBO Calculations) link
  6. Calculate pDoS/XP spectra code (under construction) link
  7. Simple script to simply pull thermodynamic data and low frequencies from log files link
  8. Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference link
  9. Codes to extract frequency data from gaussian .log files and generate vibrational spectra link
  10. Optimally Tuned Range Seperated Hybrid Functionals link
  11. Some G09 Parsers link
  12. Codes to visualise data matrices (correlation matrices/heatmaps)link
  13. Python API for analysis of Gaussian compuations - Documentation
  14. Charge arm link

QC Visualisation

  • Using AIMALL: density based visualisation
  1. download AIMALL
  2. basic instructions link
  3. AimAll with pseudo potentials link
  • ESPs and manipulating gaussian cube files
  1. Instructions for visualizing electrostatic potentials (Gaussview)link
  2. Electrostatic Potentials II (Molden) link
  3. Manipulating cube files link
  4. Format of cube files link
  5. Using A. Stone's distributed multipole analysis link
  • NCI plots
  1. get the program here: link
  2. How to install NCIPlot on your mac link
  3. Using NCIPlot link
  • MOs
  1. Visualising MOs using Jmol link

Setup and Running Classical MD Simulations

  1. DLPOLY Installation for an IMac link
  2. DL_POLY FAQs [3] from DL_POLY webpage.
  3. GROMACS installing and getting started with gromacs link
  4. using Agilio Padua force fields for ionic liquids link
  5. Packmol installing and running to generate a starting box link
  6. initial rough relaxation link
  7. GROMACS general run link
  8. GROMACS viewing data link
  9. GROMACS control file link
  10. Equilibration and production simulations link
  11. Getting the Force Field link
  12. Choosing an Ensemble link
  13. Molten Salt Simulations link
  14. Common Errors link
  15. Voids in ILslink
  16. Equilibration of [bmim][BF4] and [bmim][NO3]link
  17. Summary of discussions with Ruthlink

MD Visualisation

  • VMD: a molecular dynamics visualisation package
  1. VMD can be installed from the VMD downloads page
  2. Quick reminder link
  3. Colour in VMD link
  4. Changing the graphical representation of your structures link
  5. VMD indexing link
  6. Using scripts in VMD link
  7. Dealing with periodic boundaries and bonding (under construction) link
  8. Dealing with bonding (under construction) link
  9. How to turn a Gaussian optimization into a VMD movie link
  10. Overlapping two structures link
  • Ovito: a molecular dynamics visualisation package
  1. Download Ovito [4]
  2. Using Ovito basics link
  • SDFs
  1. How to generate SDFs link

MD Post processing

  1. Python script to convert a HISTORY file into a xyz file link
  2. Python script to reduce the number of steps in a lammps traj file link
  3. Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin link
  4. Center the trajectory at a particular atom (needs fixing) link
  5. How to generate SDFs with TRAVIS link
  6. Tcl script to follow a particular atom link

Coding

  • installing Xcode and other programming environments
  1. to use many programs you will need a compiler, this is not installed by default on your mac
  2. How to install Xcode on your mac link
  3. using MacPorts as code for managing other codes on your mac link
  4. HomeBrew and Fink are other options (HomeBrew is not advised for us)
  5. gfortran on your mac link
  6. using python on your mac link
  • EMO Code
  1. How to use Ling's emo plot codelink
  2. How to plot EMOs link
  • Jan's charge based analysis Code
  1. charge analysis link
  2. Obtaining NBO, ESP, and RESP charges link
  • Oxana's visualisation of ESPs Code
  1. Scripts for reading, saving, manipulating and visualising data from cube files link

Other Codes

  1. ADF Submission script link
  2. How to install POLYRATE link
  3. XMGRACE, gfortran, c compilers for Lion [5]

Setup and Running Ab-Initio MD Simulations

  1. CPMD: Car-Parrinello Molecular Dynamics link
  2. How to run CPMD to study aqueous solutions link
  3. How to run CP2K link

Running QM/MM Simulations in ChemShell

  1. ChemShell official website which contains the manual and a tutorial link
  2. Introduction to ChemShell - Copper in water link
  3. Defining the system: Cu2+ and its first 2 solvation shells link
  4. Defining the force field parameters link
  5. Single point QM/MM energy calculation link
  6. QM/MM Optimisation link
  7. QM/MM Molecular Dynamics link
  8. Using MolCluster link
  9. Running ChemShell link
  10. Explaining ChemShell files link
  11. Step By Step link

Admin Stuff

  1. Not used to writing a wiki, make your test runs on this page
  2. How to set-up new macs link
  3. How to switch the printer HP CP3525dn duplex on and off link
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