Difference between revisions of "Comprehensive Contents Page"

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=== Acquiring and compiling the group software ===
  
=== Acquiring and compiling the group software ===
 
* [[SVN setup]]
  
* [[SVN setup]]
  +
* [[Git Workflow]]
 
* [[Wales Group Version control]] - to keep the code standardised.
  
* [[Wales Group Version control]] - to keep the code standardised.
 
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
  
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
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=== Running on Windows ===
  
=== Running on Windows ===
  +
Not particularly recommended.
 
* [[Running Wales Group software on Windows 7]]
  
* [[Running Wales Group software on Windows 7]]
   
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* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
  
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
 
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
  
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
  +
* [[DISCOTRESS]]: A program to perform detailed quantitative analysis of a kinetic network (stationary point database)
   
 
=== Curated Examples ===
  
=== Curated Examples ===
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* [[Instanton tunneling and classical rate calculations with OPTIM]]
  
* [[Instanton tunneling and classical rate calculations with OPTIM]]
 
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
  
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
  +
* [[common setup problem : No Frequency Warning]]
   
 
=== [[PATHSAMPLE]] ===
  
=== [[PATHSAMPLE]] ===
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* [[Biomolecules in PATHSAMPLE]]
  
* [[Biomolecules in PATHSAMPLE]]
 
* [[Biomolecules in the energy landscape framework]]
  
* [[Biomolecules in the energy landscape framework]]
  +
* [[Adding several minima obtained using GMIN (maybe using BHPT) to min.data]]
 
* [[Expanding the kinetic transition network with PATHSAMPLE]]
  
* [[Expanding the kinetic transition network with PATHSAMPLE]]
 
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
  
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
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* [[Pathsampling short paths (CHARMM)]]
  
* [[Pathsampling short paths (CHARMM)]]
 
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
  
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
  +
* [[Connecting Sub-databases]]
  +
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
  +
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
  +
* [[STARTING INITIAL PATH JOBS WITH PATHSAMPLE]]: How to start initial path jobs with PATHSAMPLE if no min.data or path.info files are present.
   
 
=== [[Notes on MINPERMDIST | MINPERMDIST]] ===
  
=== [[Notes on MINPERMDIST | MINPERMDIST]] ===
   
 
=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===
  
=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===
  +
  +
=== [[DISCOTRESS | Detailed kinetic network analysis with DISCOTRESS]] ===
   
 
== Non-Group Software ==
  
== Non-Group Software ==
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* [[Simple scripts for LEaP to create topology and coordinate files]]
 
* [[Simple scripts for LEaP to create topology and coordinate files]]
 
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
  
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
  +
* [[Preparing input files for a peptide using AMBER]] - detailed guide
 
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
  
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
 
* [[Using Molfacture to edit molecules and add hydrogens]]
  
* [[Using Molfacture to edit molecules and add hydrogens]]
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* [[Evaluating different components of AMBER energy function with SANDER]]
  
* [[Evaluating different components of AMBER energy function with SANDER]]
 
* [[Mutational BH steps]]
  
* [[Mutational BH steps]]
  +
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
  +
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
 
* [[REMD with AMBER]]
  
* [[REMD with AMBER]]
 
* [[Performing a hydrogen-bond analysis]]
  
* [[Performing a hydrogen-bond analysis]]
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* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
  
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
 
* [[Rotamer moves in AMBER]]
  
* [[Rotamer moves in AMBER]]
  +
* [[Creating mismatched DNA duplex using NAB]]
   
 
=== [[aux2bib]] ===
 
=== [[aux2bib]] ===
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* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
  
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
 
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
  
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
  ⚫
=== [[VASP]] ===
  +
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like
  +
  +
VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'
  +
  +
POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via
  +
  +
module load anaconda/python3/5.3.0
  +
  +
pip install ase --user
  +
  +
ase-gui POSCAR1.vasp &
  +
  +
which assumes that ~/.input/bin is in your $PATH environment variable.
  +
   
 
=== [[VMD]] ===
  
=== [[VMD]] ===
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* [[Decoding heat capacity curves]]
  
* [[Decoding heat capacity curves]]
 
* [[Differences from Clust]]
  
* [[Differences from Clust]]
−
* [[group Mendeley account]]
  
 
* [[Fixing thunderbird links]]
  
* [[Fixing thunderbird links]]
 
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
  
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
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* [[Tardis scheduling policy]]
  
* [[Tardis scheduling policy]]
 
* [[Zippo Sicortex machine]]
  
* [[Zippo Sicortex machine]]
  +
* [[Beginner's guide to working in Wales group]]
−  
⚫
=== People ===
  
−
* [[Catherine Pitt]]
  
−
* [[Chris Whittleston]]
  
−
* [[Halim Kusumaatmaja]]
  
−
* [[James Spencer]]
  
−
* [[Kenji Mochizuki]]
  
−
* [[Sandeep Somani]]
  
−
* [[Scott Olesen]]
  
−
* [[User:Vr274 | Victor Ruehle]]
  
   
 
== Useful linux stuff ==
  
== Useful linux stuff ==
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* [[submitting jobs, interactively or to a cluster queue system]]
  
* [[submitting jobs, interactively or to a cluster queue system]]
 
* [[identifying job on a node]] - if you need to kill only one of few running jobs
  
* [[identifying job on a node]] - if you need to kill only one of few running jobs
  +
* [[getting started with SLURM]]
 
* [[a guide to using SLURM to run PATHSAMPLE]]
  
* [[a guide to using SLURM to run PATHSAMPLE]]
 
* [[a guide to using SLURM to run GPU jobs on pat]]
  
* [[a guide to using SLURM to run GPU jobs on pat]]
  +
* [[managing interactive jobs on cluster]]
   
 
===Miscellaneous/uncategorised===
  
===Miscellaneous/uncategorised===
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* [[printing files from the command line using 'lpr']]
  
* [[printing files from the command line using 'lpr']]
 
* [[uploading non image files to the wiki]]
  
* [[uploading non image files to the wiki]]
−
* [[group Mendeley account]]
  
−  
−
== Group practice ==
  
−  
−
If you add a page under here please prefix the name with Wales or similar to avoid confusion with pages that apply to the whole sector.
 
−  
−
* [[Wales group calendars]] - so you always know who is around to help you debug, or when you should not come into work wearing your PJs.
  
−
* [[Animated GIF on the group website]] - how to update it when needed
  
−
* [[Google Drive folder]] - ask someone in the group to give you access
  
−
* [[Adding example input for Wales group programs | adding example input for your work ]]
  
−
* [[Wales Group Conventions when using LaTex | conventions when using LaTex]]
 
−
* [[Using inkscape for LaTeX-rendered text]]
  
−
* [[Wales Group Fortran conventions for group software | Fortran conventions for group software]]
  
−
* [https://www.thc.org/root/phun/unmaintain.html Guide on how to write unmaintainable code] - not intended to inspire you!
  
−
* [[Wales Group Version control | version control ]]
  
−
* [[Papers in preparation]]
  
−
* [[Group wish list]] - would like to see a new feature in GMIN? Can you think of a way to improve things but you're not sure how to do it? Add your thoughts here!
  
−
* [[Bug hunting tips for group code]]
  
−
* [[Purchasing tips, including travel]]
  
−
* [[Satisfying funder Open Data policies when you publish]]
  
−
* [[Wales Group Fortran conventions for group software]]
  
−
* [[group Mendeley account]]
  
−
* [[Google Drive folder]]
  
−
* [[IT Equipment wishlist]]
  
−
* [[Open data case study: RNA CUG]]
  
−
* [[Updating the Covers Collage on the Group Website]]
  
−
* [[Visitor policy]]
  
   
 
== Compiler Flags ==
  
== Compiler Flags ==

Latest revision as of 11:17, 28 October 2021

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

Getting Started

Wales Group provides good step-by-step instructions. Relevant pages are:

Acquiring and compiling the group software

Maintaining code health

Collaborators without access to the SVN repository

For licensing reasons, some code cannot be included in the Wales Group public tarball.

If a collaborator has a CHARMM or AMBER licence, we do maintain separate tarballs which include the CHARMM, AMBER and CHARMM+AMBER source and interfaces. These are not linked anywhere on the website and require a username (wales) and password (group) to download:

Running on Windows

Not particularly recommended.

Wales Group Programs

Programs

  • GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
  • OPTIM: A program for optimizing geometries and calculating reaction pathways.
  • PATHSAMPLE: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
  • Pele: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
  • DISCOTRESS: A program to perform detailed quantitative analysis of a kinetic network (stationary point database)

Curated Examples

git clone https://github.com/wales-group/examples.git

Useful Notes on Wales Group Programs and Subroutines

GMIN

Scripts

  • makerestart: A bash script to automatically set up a GMIN restart run
  • progress A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

Useful info for coding GMIN

Projects

OPTIM

PATHSAMPLE

MINPERMDIST

QCI

Detailed kinetic network analysis with DISCOTRESS

Non-Group Software

AMBER

Molecular dynamics simulation program and associated force fields.

aux2bib

To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.

CamCasp

Cambridge package for Calculation of Anisotropic Site Properties From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'

CPMD

Implementation of DFT for ab-initio molecular dynamics.

CHARMM

Molecular dynamics simulation program and associated force fields.

disconnectionDPS

Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.

DMACRYS

Package which models crystals of rigid molecules.

GAMESS

General ab initio quantum chemistry package.

Gaussian

General purpose package for computational chemistry calculations.

gnuplot

Open source graphing program.

GROMACS

Molecular dynamics package.

HiRE-RNA

High-res course-grained energy model for RNA.

latex2html

Script which converts latex documents into HTML pages.

MMTSB-toolset

Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.

OPEP

OPEP is a coarse-grained force field providing a potential for proteins and RNA.

pgprof

Profiler for portland-compiled codes

Pymol

Molecular visualisation program.

VASP

OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.


VMD

Molecular visualisation program.

xfig

Open source vector graphics editor

Xmakemol

Program for visualising atomic and molecular systems.

xmgrace

2D plotting tool.

Theoretical/Mathematical Notes

Angle-axis notes

Rigid Bodies

Useful Scripts

See also the SCRIPTS/ directory in the SVN repository!

Useful links

  • A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)
  • The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

Miscellaneous

Useful linux stuff

Basics

Remote access

Find and replace

File manipulation

Cluster queues

Miscellaneous/uncategorised

Compiler Flags

SuSE


--adk44 17.00, 9 May 2019 (BST)

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