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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
  3. Moving large files and directories around link

HPC Resources

  1. Getting started and introduction to the HPC: link
  2. Hunt group HPC resources and run scripts link
  3. How to use gaussview directly on the HPC link
  4. Link to RCS (HPC) tips page link
  5. How to run jobs interactively link
  6. Computing resources available in the chemistry department link
  7. New gf script (more convenient job submitting) link
  8. Retired: How to make qsub more comfortable (gfunc) link
  9. Tired of entering your password all the time: set up a SSH keypair link
  10. How to make ssh more comfortable link
  11. How to comfortably search through old BASH commands link
  12. Using VPN from home, for Sierra follow the college instructions link
  13. How to connect to HPC directory on desktop for file transfers link
  14. How to set-up remote desktop link
  15. 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
  4. Box size for MD simulations of 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. problems with scf convergence link
  9. manipulating checkpoint files link
  10. for NMR calculations look here: Chemical Shift Repository
  11. Population and charge analysis link

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
  9. Multidimensional Scans of Internal Coordinates link
  10. Conformational search of atomic and molecular clusters with ABCluster link

Solvation

  1. Using the SMD model 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

Python and Python codes

  1. Using and installing python link
  2. Python toolkit currently focussed towards gaussian analysis link
  3. Standalone python scripts and analysis:
    • List the energy for each step of a gaussian log file, find the lowest energy and produce a quick graph in kJ/mol link
    • Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job link
    • Extract last Standard Orientation structure of gaussian log file link
    • Extract last structure of gaussian optimisation and build a freq com file for job with PP link
    • Extract each optimised step from a scan into xyz coordinate file link
    • Extract thermodynamic data and low frequencies from log files (python 2) link
    • Extract thermodynamic data and low frequencies from log files to enter into excel template provided for the database (python 3) link
    • Extract geometry and charges (ESP) into a .pdb file for visualising in VMD link
    • Codes to extract CHELPG and NBO charge values to excel link
    • Extract ESP and NBO charges link
    • Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference link
    • Codes to extract frequency data from gaussian .log files and generate vibrational spectra link
    • Codes to visualise data matrices (correlation matrices/heatmaps)link
    • Python API for analysis of Gaussian computations - Documentation
    • Charge arm link
    • Extract the MO orbital energies and concert to eV link

Other codes

  1. Extract E2 Values (From NBO Calculations) link
  2. Calculate pDoS/XP spectra code (under construction) link
  3. Optimally Tuned Range Separated Hybrid Functionals link
  4. Some G09 Parsers link

QC Visualisation

  • Using AIMALL: density based visualisation
  1. download AIMALL
  2. once downloaded and installed you need to send tricia your aimall-serialnumber.txt file, and she will arrange for a aimallpro.lic or license file for you
  3. basic instructions link
  4. AimAll with pseudo potentials link
  5. AIMAll 19.10.12 on iMacs 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

dl_poly

  1. DLPOLY_4.0 Installation for an IMac link
  2. DLPOLY_Classic Installation for an IMac link
  1. DL_POLY FAQs [3] from DL_POLY webpage.
  2. some basics for getting started using DL_POLY link
  3. control file basics link
  • useful links
https://www.ccp5.ac.uk
https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx
dlpoly4 user manual
javagui user manual
dlpoly ftp server
you can find test files in DL_POLY_4.0/DATA
more info about the dlpoly test files link

gromacs

  1. GROMACS installing and getting started with gromacs link
  2. using Agilio Padua force fields for ionic liquids link
  3. Packmol installing and running to generate a starting box link
  4. initial rough relaxation link
  5. GROMACS general run link
  6. GROMACS viewing data link
  7. GROMACS control file link
  8. Equilibration and production simulations link

general

  1. Getting the Force Field link
  2. Choosing an Ensemble link
  3. Molten Salt Simulations link
  4. Common Errors link
  5. Equilibration of [bmim][BF4] and [bmim][NO3]link
  6. 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
  • Python Genereal
  1. General python recommendations and set up link
  2. Analysis toolkit mainly geared towards processing Gaussian calculations link

Other Codes

  1. ADF Submission script link
  2. How to install POLYRATE link
  3. XMGRACE, gfortran, c compilers for Lion [5]
  4. Run SAPT calculations using Psi4 link

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

Tcl-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

Py-chemshell

  1. Compiling Chemshell and required programs []
  2. The DL_POLY_4 manual is available for download at this link [6]
  3. Molecular Mechanics computation with DL_POLY [7]
  4. Basic QM/MM single point and optimisations [8]
  5. Visualise optimisation trajectories in VMD [9]
  6. Computing Mulliken charges and creating .wfn inputs for AIM analysis [10]

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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