Difference between revisions of "Wales Group"

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import>Csw34
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* [[printing files from the command line using 'lpr']]
 
* [[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!)]]
 
* [[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]]
 
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]
 
* [[data manipulation using 'sed']]
 
* [[data manipulation using 'sed']]

Revision as of 13:13, 29 April 2008

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

Group practice