Comprehensive Contents Page

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

• SVN setup
• Git Workflow
• Wales Group Version control - to keep the code standardised.
• Theory Sector SVN Page - some useful general information on SVN commands.
• Compiling Wales Group codes using cmake - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
• ElaborateDiff

Maintaining code health

• Jenkins CI - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
• https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
• Branching and Merging
• Cmake interface building
• Installing python modules
• Revamping the modules system

Collaborators without access to the SVN repository

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

• http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes GMIN, OPTIM and PATHSAMPLE.

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:

• CHARMM
• AMBER
• AMBER+CHARMM

Running on Windows

Not particularly recommended.

• Running Wales Group software on Windows 7

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

• https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
• http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
• https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
• https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:

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

Useful Notes on Wales Group Programs and Subroutines

GMIN

• Adding a model to GMIN - rough outline of the subroutines that need to be changed to add a new model to GMIN
• Compiling GMIN using cmake
• Selecting search parameters for GMIN
• Global optimization of biomolecules using CHARMM
• Global optimization of biomolecules using AMBER9
• Global optimization of biomolecules using AMBER9 with Structural Restraints
• Calculating binding free energy using the FSA method
• Restarting a GMIN run from a dump file
• Using the implicit membrane model IMM1
• Running a Go model with the AMHGMIN
• Running a G\=o model with the AMHGMIN
• Ligand binding-mode searches with HBONDMATRIX
• Compiling and using GMIN with QUIP
• Using GMIN and OPTIM with GPUs
• Using GMIN to generate endpoints
• Using GMIN to generate endpoints (CHARMM)
• Generating a GMIN Eclipse project
• Mutational BH steps
• Biomolecules in the energy landscape framework
• DMAGMIN setup
• Keywords
• PYGMIN & DMACRYS
• Rotamer moves in AMBER
• Python interface for GMIN/OPTIM

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

• Program flow - contains information about what the various files in GMIN do and what order they're called.
• amberinterface

Projects

• GMIN MOVES module
• GMIN SANITY module
• GMIN TESTS module
• CAMSHIFT

OPTIM

• Adding a model to OPTIM - rough outline of the subrounties that need to be changed to add a new model to OPTIM
• Adding partially finished OPTIM stationary points to a PATHSAMPLE database
• perm-pdb.py: A python program that creates a perm.allow file for use with OPTIM and PATHSAMPLE.
• visualising normal modes using VMD and OPTIM
• Compiling OPTIM using cmake
• OPTIM/Q-Chem Tutorial
• OPTIM and PY ellipsoids tutorial
• OPTIM output files
• Minimizing a structure using OPTIM and AMBER9
• Minimizing a structure using OPTIM and CHARMM
• Creating movies (.mpg) of paths using OPTIM
• Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
• Debugging odd transition states in OPTIM
• Connecting two minima with a pathway - step by step
• Compiling and using OPTIM with QUIP
• Running an Gaussian03 interfaced OPTIM job
• The effect of calculating less than the maximum number of eigenvalues using ENDHESS n
• Biomolecules in the energy landscape framework
• BLJ60 example setup
• Finding an initial path with OPTIM and starting up PATHSAMPLE
• Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)
• Python interface for GMIN/OPTIM
• Thomson problem in OPTIM
• Instanton tunneling and classical rate calculations with OPTIM
• Loading OPTIM's min.data.info files into PATHSAMPLE
• common setup problem : No Frequency Warning

PATHSAMPLE

• Adding a model to PATHSAMPLE - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
• Alternatively, making the initial path with PATHSAMPLE itself
• Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)
• perm-pdb.py: A python program that creates a perm.allow file for use with OPTIM and PATHSAMPLE.
• dijkstra_test.py: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
• Compiling PATHSAMPLE using cmake
• IMPORTANT: Using PATHSAMPLE safely on sinister
• Adding a model for PATHSAMPLE
• List of output files for PATHSAMPLE
• Using BHINTERP to find minima between two end points
• Finding an initial path between two end points (minima)
• Adding partially finished OPTIM stationary points to a PATHSAMPLE database
• Optimising a path
• Fine tuning UNTRAP - ensuring that it picks sensible minima
• Calculating rate constants (GT and fastest path)
• Calculating rate constants (SGT, DGT, and SDGT)
• Identifying the k fastest paths between endpoints using KSHORTESTPATHS
• Removing minima and transition states from the database
• Relaxing existing minima with new potential and creating new database
• Relaxing existing transition states with new potential and creating new database
• If things go wrong...
• If you lost file min.data, but still you have points.min
• path.info file is not read, causes PATHSAMPLE to die
• BLJ60 example setup
• When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path
• Biomolecules in PATHSAMPLE
• 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 (CHARMM)
• Finding an initial path with OPTIM and starting up PATHSAMPLE
• Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)
• Pathsampling short paths
• Pathsampling short paths (CHARMM)
• 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.

Non-Group Software

AMBER

Molecular dynamics simulation program and associated force fields.

• AMBER
• AMBER tutorials - recommended reading for ANYONE using AMBER!
• Notes on AMBER 12 interface
• Using AMBER 14 on the GPU and compute clusters
• Generating parameters using AMBER's built in General Forcefield (gaff)
• Generating parameters using RESP charges from GAMESS-US
• Simple scripts for LEaP to create topology and coordinate files
• 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
• Using Molfacture to edit molecules and add hydrogens
• Preparing an AMBER topology file for a protein plus ligand system - step by step guide
• Symmetrising AMBER topology files - step by step guide for symmetrising a complex protein+ligand system
• Producing a PDB from a coordinates and topology file - using amdpdb
• Running GMIN with MD move steps AMBER
• Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
• Evaluating different components of AMBER energy function with SANDER
• 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
• Performing a hydrogen-bond analysis
• Alternatively, making the initial path with PATHSAMPLE itself
• Biomolecules in the energy landscape framework
• 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
• Creating mismatched DNA duplex using NAB

aux2bib

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

• Get script here

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).'

• CamCASP home
• CamCASP/Programming
• CamCASP/Programming/5/example1
• CamCASP/Notes
• CamCASP/Bugs
• CamCASP/ToDo/diskIO
• CamCASP/ToDo/Memory
• CamCASP/CodeExamples/DirectAccess

CPMD

Implementation of DFT for ab-initio molecular dynamics.

• Home Page
• CPMDInput

CHARMM

Molecular dynamics simulation program and associated force fields.

• CHARMM
• Generating pdb, crd and psf for a peptide sequence
• Converting between '.crd' and '.pdb'
• Calculating energy of a conformation
• Calculating molecular properties
• Calculating order parameters
• CAMSHIFT
• Setting up (CHARMM) - step by step guide to prepare and then symmetrise a simple (protein-only) system
• If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)
• Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)
• Minimizing a structure using OPTIM and CHARMM
• Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)
• Expanding the kinetic transition network with PATHSAMPLE (CHARMM)
• Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)
• Pathsampling short paths (CHARMM)

disconnectionDPS

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

• Constructing Free Energy Disconnectivity Graphs

DMACRYS

Package which models crystals of rigid molecules.

• Home Page
• DMACRYS interface
• DMAGMIN setup
• PYGMIN & DMACRYS

GAMESS

General ab initio quantum chemistry package.

• GAMESS

Gaussian

General purpose package for computational chemistry calculations.

• Running an Gaussian03 interfaced OPTIM job

gnuplot

Open source graphing program.

• gnuplot
• Plotting a quick histogram in gnuplot using the raw data
• Plotting data in real time
• Linear and non-linear regression in gnuplot

GROMACS

Molecular dynamics package.

• Installing GROMACS on Clust
• External tutorials
• More external tutorials

HiRE-RNA

High-res course-grained energy model for RNA.

• Explanatory Paper

latex2html

Script which converts latex documents into HTML pages.

• Get script here

MMTSB-toolset

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

• Documentation
• External tutorials
• Installing and setting up the MMTSB toolset
• REX (Replica EXchange MD) with the MMTSB-toolset

OPEP

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

• OPEP file generator here
• Biomolecules in the energy landscape framework

pgprof

Profiler for portland-compiled codes

• Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays

Pymol

Molecular visualisation program.

• PyMOL
• PyMOL Community Wiki
• loading AMBER prmtop and inpcrd files into Pymol
• producing sexy ray-traced images
• advanced colouring
• Installing python modules
• PYGMIN & DMACRYS
• 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

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.

• Documentation
• External tutorials
• using VMD to display and manipulate '.pdb' files
• loading coordinate files into VMD with the help of an AMBER topology file e.g. to visualise the results of a GMIN run using AMBER9
• visualising normal modes using VMD and OPTIM
• path2pdb.py: A python program to convert path.info to path_all.pdb - you can easy visualize your path in VMD :)
• path2xyz.py: A python program to convert path.info to path_all.xyz
• extractedmin2pdb.py: A python program to convert exctractedmin to PDB format
• Useful .vmdrc file
• plotGMINms.tcl: a tcl script for plotting ellipsoids in VMD.
• VMD script to annotate each frame of a trajectory

xfig

Open source vector graphics editor

• Convert eps to pdf

Xmakemol

Program for visualising atomic and molecular systems.

• XMakemol

xmgrace

2D plotting tool.

• Xmgrace

Theoretical/Mathematical Notes

• Density of states and thermodynamics from energy distributions at different temperatures
• Ellipsoid.model
• Ellipsoid.model.xyz
• Ellipsoid.xyz
• Gencoords
• GenCoords
• GenCoords Models
• Rotamer moves in AMBER
• Thomson problem in OPTIM

Angle-axis notes

• Angle-axis framework
• Computing normal modes in angle-axis

Rigid Bodies

• Automatic Rigid Body Grouping
• Rigid body input files for proteins using genrigid-input.py
• Local Rigid Body Framework
• Local rigid body in OPTIM

Useful Scripts

• 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-pdb.py: A python program that creates a perm.allow file for use with OPTIM and PATHSAMPLE.
• path2pdb.py: A python program to convert path.info to path_all.pdb - you can easy visualize your path in VMD :)
• path2xyz.py: A python program to convert path.info to path_all.xyz
• dijkstra_test.py: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
• extractedmin2pdb.py: A python program to convert exctractedmin to PDB format
• colourdiscon.py: A python program for sorting input for disconnectivity graphs
• pdb_to_movie.py: A python program to create an AMH movieseg file from a PDB file
• 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
• recommended bash aliases
• David's .inputrc file
• Useful .vmdrc file
• Density of states and thermodynamics from energy distributions at different temperatures
• GenCoords: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
• plotGMINms.tcl: a tcl script for plotting ellipsoids in VMD.

See also the SCRIPTS/ directory in the SVN repository!

• Computing CHARMM FF energy using GMIN, MMTSB and CHARMM - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
• Automatic Rigid Body Grouping
• ElaborateDiff
• Parameter-scanning script
• Pdb to movie.py
• VMD script to annotate each frame of a trajectory

Useful links

• The Theory Compute Clusters support page. Contains useful cluster specific information, including example job submission scripts.

• 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

• Animated GIF on the group website
• Backup strategy
• Chain crossing
• Computer Office services
• Computing values only once
• Decoding heat capacity curves
• Differences from Clust
• 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)
• Intel Trace Analyzer and Collector
• LDAP plans
• Lapack compilation
• Mek-quake Queueing system
• Mek-quake initial setup notes
• New mek-quake
• Maui compilation
• Torque and Maui
• Mercurial
• Migrating to the new SVN server
• NECI Parallelization
• Optimization tricks
• Other IT stuff
• Porfuncs Documentation
• Progress
• Proposed changes to backup and archiving
• Rama upgrade
• Remastering Knoppix
• See unpacked nodes
• Tardis scheduling policy
• Zippo Sicortex machine
• Beginner's guide to working in Wales group

Useful linux stuff

Basics

• basic linux commands everyone should know!
• piping and redirecting output from one command or file to another - how to save yourself hours!
• bash loop tricks
• bash history searching

Remote access

• setting up aliases to quickly log you in to a different machine
• transfering files to and from your workstation -using scp or rsync
• using 'ssh-keygen' to automatically log you into clusters from your workstation (no more typing in your password!)
• mounting sharedscratch locally

Find and replace

• short 'sed' examples
• quick guide to awk
• short 'awk' examples

File manipulation

• sorting a file by multiple columns
• using tar and bzip2 to compress/uncompress files
• conversion between different data file formats -'almost one-line' scripts
• conversion between different image file formats - the convert command
• removing an excessive number of files from a directory - when 'rm' just isn't enough

Cluster queues

• 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
• getting started with SLURM
• a guide to using SLURM to run PATHSAMPLE
• a guide to using SLURM to run GPU jobs on pat
• managing interactive jobs on cluster

Miscellaneous/uncategorised

• installing packages on your managed CUC3 workstation
• running programs in the background - so you can use your shell for other things at the same time
• finding bugs in latex documents that will not compile
• printing files from the command line using 'lpr'
• uploading non image files to the wiki

Compiler Flags

• Compiler Flags
• Blacklisting Compilers
• Lapack compilation
• Pdb to movie.py
• Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays

SuSE

• Upgrading destiny
• Upgrading sword
• SuSE 10.1 workstation image
• SuSE 10.2 workstation image
• SuSE 10.3 workstation image
• SuSE 11.1

--adk44 17.00, 9 May 2019 (BST)