HRG:HuntResearchGRoup

Hunt Research Group Wiki

Report and Paper Writing

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

Data Base

1. Which files to store on the database and database template link

Key Papers

1. Best-Practice Protocols for choosing method and basis doi
2. Status and Challenges of Density Functional Theory doi
3. Meta study on DFT functionals doi
4. M06 suite of DFT functionals doi
5. SMD for ILs doi
6. Box size for MD simulations of ILs doi

HPC Resources

1. Getting started and introduction to the HPC: link
2. Running jobs on the HPC: link
3. How much memory (and disk) to use: link
4. How to start an interactive session: link
5. How to set-up remote desktop link
6. How to use cloud storage resources link

Using Windows PCs

1. use MobaXTerm link
2. use Putty link
3. very basic using a Terminal on a Windows PC external link
4. install a Linux distribution link
5. How to fix Windows files under UNIX link

Tips and Tricks

1. Tired of entering your password all the time: set up a SSH keypair link
2. How to make ssh more comfortable link
3. How to comfortably search through old BASH commands link
4. A terminal emulator capable of splitting into multiple screens link

ORCA 6.0

1. This section is about using ORCA 6.0 on the HPC (Raapoi) link
2. Using different basis sets and pseudopotentials for heavy elements in ORCA link
3. Plotting MOs with ORCA in GaussView format link
4. Memory Specification in ORCA 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. beginners starting from a chemdraw structure link
4. optimisation errors and problems link
5. partial optimisations and scans link
6. general procedure for locating transition state structures link
7. how to include dispersion link
8. basic ONIOM (Mechanical Embedding) link
9. problems with scf convergence link
10. creating formatted checkpoint files link
11. generating and manipulating cube files link
12. for NMR calculations look here: Chemical Shift Repository
13. Population and charge analysis link
14. how to run NBO7 on the HPC link
15. G03 Manual

Gaussian Advanced

1. how to run at a higher temperature link
2. correcting the entropy due to low modes link
3. how to run NBO5.9 on the HPC link
4. generating natural transition orbitals link
5. computing excited state polarisabilities link
6. dipoles in Gaussian link
7. molecules in an electric field link
8. computing deuterated and/or anharmonic spectra link
9. conformational search of atomic and molecular clusters with ABCluster link
10. old:systematic conformational scan for ion-pair dimers link
11. old: optimisation of charged molecules in an electric field link
12. old: multidimensional Scans of Internal Coordinates link

Solvation

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

QC Visualisation

1. 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 volume / surface area calculations link
   5. AimAll with pseudo potentials link
   6. AIMAll 19.10.12 on iMacs link
2. Using Multiwfn: density based visualisation
   1. Download Multiwfn link
   2. Installation of Multiwfn on Mac link
   3. Finding sigma hole (Vs,max and Vs,min values) link
3. ESPs and 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
4. NCI Plots
   1. How to install NCIPlot on your mac link
   2. Using NCIPlot link
5. Jmol Visualisations
   1. Jmol basics link
   2. Visualising MOs using Jmol link
   3. Using Jmol to make a structure animation link
   4. Using Jmol to overlap structures link
6. 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

Other Programes

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

Coding

• installing Xcode and other programming environments

1. 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

1. EMO Code
   1. How to use Ling's emo plot codelink
   2. How to plot EMOs link

1. Jan's charge based analysis Code
2. charge analysis link
3. Obtaining NBO, ESP, and RESP charges link

1. Oxana's visualisation of ESPs Code
   1. Scripts for reading, saving, manipulating and visualising data from cube files link

Python scripts

• note: scripts with "D" in front are those made to run on groups of files

they can be for when you have a large number of files from a crest run

they can be for use within a single directory, running on all files in that directory

made to be used with a set of specific gaussian log files, Tricia's ones are made to work on files with a structured naming sequence, for example struc_xx_B3LYP_D3BJ_6311pGdp_opt.log where xx is the individual number

1. for set-up and running
   1. XX_sumbit.py script: Code to auto-create a batch script link
   2. Dsumbit.py script: Code to auto-create a batch script for ALL the com files in a partucluar directory and submit them to the que link
   3. get_energy.py script: Check a job while it is running, plot energy, find lowest force link
   4. tlog.py script: Check a job while it is running by using tail, printing Max force, Max displacement, Energy and saving a version to your home directory link
2. to extract structures
   1. extract_structure.py script: Extract last Standard Orientation structure of gaussian log file link
   2. Dextract_structure.py script: Extract last Standard Orientation structure of multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log link
   3. extract_geom.py script: Extract Optimized Geometry Gaussian/ORCA log file into an .xyz or .com file link
   4. extract_steps.py script: Extract each optimised step from a scan into xyz coordinate file link
   5. extract_crest_conf.py script: Extract given structure from a CREST conformer file and save to a *.xyz file (useful for using with Jmol) link
3. to build new files from data or existing files
   1. build_freq.py script: Build a frequency file from an optimisation file ready to submit, this will require editing for your particular job link
   2. Dbuild_freq.py script: Extract last structure of gaussian optimisation and build a freq com file for multiple gaussian log files of the form struc_xx_B3LYP_D3BJ_6311pGdp_opt.log link
   3. symb_zmat.py script: Generate a symbolic z-matrix, requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words link
   4. pos_zmat.py script: Orientate the molecule along a specific axis, rotate by a defined angle and or fix a particular atom as the origin. Requires you to use extract_structure.py and form a *.inp file with the xyz coords and a set of command words, generates a symbolic z-matrix link
4. to extract Thermochem data
   1. getdata.py script: Extract thermodynamic data and low frequencies from a single log file into a formatted line to copy and paste into an excel files for the database link
   2. Dgetdata.py script: Extract thermodynamic data and low frequencies from all the log files in a directory into a csv file for the database (Tricia) link
   3. Dget_frequencies_data.py script: Extract thermodynamic data and low frequencies from all the log files in a directory to a csv file for the database (Muhammad) link
5. to extract Charges
   1. Codes to extract CHELPG and NBO charge values to excel (Irelie) link
   2. extract_charges.py Extract ESP and NBO charges link
   3. Instructions for how to extract geometry and charges (ESP) into a .pdb file for visualising in VMD, especially if you want a blue-red colour variation rather than gaussviews red-greeen link
   4. Charge arm link
6. Other quantities
   1. extract_aim.py script: Extract volume data from AIMALL sumviz files link
   2. Script to extract frequency data from gaussian .log files and generate vibrational spectra link
   3. Extract the MO orbital energies and concert to eV link
   4. Calculate pDoS/XP spectra code link
7. Historical codes
   1. freq.py historical python2 script" Extract thermodynamic data and low frequencies from log files link
   2. Codes to visualise data matrices (correlation matrices/heatmaps)link
   3. Python toolkit currently focussed towards gaussian analysis link
   4. Extract E2 Values (From NBO Calculations) link
   5. Optimally Tuned Range Separated Hybrid Functionals link
   6. Some G09 Parsers link

Setup and Running Classical MD Simulations

1. dl_poly
   1. DLPOLY_4.0 Installation for an IMac link
   2. DLPOLY_Classic Installation for an IMac link
   3. DL_POLY FAQs [2] from DL_POLY webpage.
2. some basics for getting started using DL_POLY link
   1. control file basics link
   2. 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

1. 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

1. 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 [3]
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

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
   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

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

Other Resources

1. Solving the angular part of the Schrödinger equation for a hydrogen atom link (notes by Vincent)
2. DFT Workshop Notes [9]
3. Cl- in water link
4. The use of Legendre time correlation functions to study reorientational dynamics in liquids link
5. Isotope effects, how to calculate partition factors, d and D-values link
6. Schrodinger workshop 1 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
4. Mac user admin basics link
5. How to access DROBO link
6. Moving large files and directories around link

Old Imperial

1. Old Imperial HPC information link
2. Old Imperial use gaussview directly on the HPC link
3. Old Imperial How to connect to HPC directory on desktop for file transfers link
4. Old Imperial How to run jobs interactively link
5. Old Imperial Computing resources available in the chemistry department link
6. Old Imperial New gf script (more convenient job submitting) link
7. Old Imperial How to make qsub more comfortable (gfunc) link
8. Old Imperial How to use a slimmed down terminal on your IPhone link