Wales Group

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.

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.

• 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

Other useful software

• REX (Replica EXchange MD) with the MMTSB-toolset
• gnuplot
• VMD
• Pymol

Useful scripts

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