Difference between revisions of "Wales Group"
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Members: |
Members: |
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Revision as of 13:51, 29 April 2008
[[Image:Walesgroup1.jpg]|thumb|The usual suspects at Byron's Pool after Vanessa's viva|400px|right]] 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
Useful software
Useful scripts
- perm-prmtop.py: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange.
Useful linux stuff
- basic linux commands everyone should know!
- setting up aliases to quickly log you in to a different machine
- using 'scp' to transfer files to and from your workstation
- 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
- data manipulation using 'sed'
- data manipulation using 'awk'
- using tar and gzip to compress/uncompress files
Group practice
- conventions when using LaTex - including the use of 'psfrag'
- Fortran conventions for group software