Difference between revisions of "Wales Group"

Revision as of 14:21, 13 May 2008

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

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
makerestart: A bash script to automatically set up a GMIN restart run
recommended bash aliases
David's .vimrc 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 -'almost one-line' scripts
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

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.

@@ Line 39: / Line 39: @@
 * [[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''