Wales Group

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

Members:

• Dr David J. Wales
• Szilard Fejer
• Chris Whittleston
• Hayley McKay
• Dr Joanne Carr
• Dr Dwaipayan Chakrabarti
• Dr Edyta Malolepsza
• Dr Birgit Strodel

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

The official documentation can be found here. It is highly reccomended 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.

• 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
• xfig
• disconnectionDPS

Useful scripts

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

Useful linux stuff

• basic linux commands everyone should know!
• piping and redirecting output from one command or file to another - how to save yourself hours!
• setting up aliases to quickly log you in to a different machine
• transfering files to and from your workstation -using scp
• printing files from the command line using 'lpr'
• using 'ssh-keygen' to automatically log you into clusters from your workstation (no more typing in your password!)
• 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
• short 'sed' examples
• short 'awk' examples
• using tar and gzip to compress/uncompress files
• conversion between different data file formats
• conversion between different image file formats - the convert command
• submitting jobs, interactively or to a cluster queue system
• running programs in the background - so you can use your shell for other things at the same time

Group practice

• conventions when using LaTex
• Fortran conventions for group software
• version control