Wales Group

The usual suspects at Byron's Pool after Vanessa's viva

Mike bringing American passion to English sport. It's just not Cricket!

Members:

• Prof David J. Wales
• Szilard Fejer
• Chris Whittleston
• Hayley McKay
• Livia Bartok-Partay
• Marianne Bauer
• Dr Joanne Carr
• Dr Dwaipayan Chakrabarti
• Dr Edyta Malolepsza
• Dr Birgit Strodel
• Dr Jason Green
• Dr Erwin Lijnen

with

• Celebrity batsman, Dr Mike Prentiss

This page is intended to be an index of useful info concerning group practice and use of software including tutorials. Please feel free to add any notes you have on software use and especially on common problems you encounter. Any links in red have not been written yet so if you get time, please fill in some of the gaps!

Group software

Our software is managed under Subversion (SVN) version control. For information on how to set up your SVN details and access the code, see the SVN setup page. Tips on good practice when using SVN can be found on the group version control page. It is highly recommended that you read this once you have set up your details. Once you're up and running, you should definitely take a look at the Theory Sector SVN Page which is chock full of useful info on the commands you'll be using on a regular basis.

The official documentation can be found here. It is highly recommended that before you start any jobs, you check the documentation to make sure you understand what each keyword you have specified does and if it's necessary! The links below provide a few working examples for each program the group uses, from initial setup to job submission.

Showing your output to DJW is particularly important when you are starting to use one of these programs for the first time. Always question any output that looks suspicious. The below links provide more information on each piece of code, including worked tutorials and general help!

• 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

Useful software

• CHARMM
• AMBER
• REX (Replica EXchange MD) with the MMTSB-toolset
• gnuplot
• VMD
• Pymol
• xmgrace
• latex2html
• aux2bib - to generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
• xfig
• disconnectionDPS
• Xmakemol
• GAMESS

Useful scripts

• perm-prmtop.py: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange.
• 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
• 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 .vimrc file
• David's .inputrc file

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!

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

• 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
• the many uses of 'rm' - getting rid of your files safely
• 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
• see unpacked nodes - if you want to see which nodes aren't currently packed so that you know which ones to submit to

Miscellaneous/uncategorised

• 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'

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.

• SVN best practice - before you commit anything, make sure you read this!
• 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.
• adding example input for your work
• conventions when using LaTex
• Fortran conventions for group software
• version control
• 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!
• Chris's 'all you can eat' tips - by popular request
• Bug hunting tips for group code