Difference between revisions of "Wales Group"
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* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange. |
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange. |
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| − | * [[path2pdb.py]]: A python program to convert ''path.info'' file from PATHSAMPLE and AMBER9 |
+ | * [[path2pdb.py]]: A python program to convert ''path.info'' file from PATHSAMPLE and AMBER9 into ''path_all.pdb'' - you can easy see your path in VMD :) |
| − | * [[path2xyz.py]]: A python program to convert ''path.info'' file from PATHSAMPLE and AMBER9 |
+ | * [[path2xyz.py]]: A python program to convert ''path.info'' file from PATHSAMPLE and AMBER9 into ''path_all.xyz'' |
| − | * [[extractedmin2pdb.py]]: A python program to convert exctractedmin from PATHSAMPLE and AMBER9 |
+ | * [[extractedmin2pdb.py]]: A python program to convert exctractedmin file from PATHSAMPLE and AMBER9 to PDB file |
== Useful linux stuff == |
== Useful linux stuff == |
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Revision as of 14:21, 30 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. 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
- 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 file from PATHSAMPLE and AMBER9 into path_all.pdb - you can easy see your path in VMD :)
- path2xyz.py: A python program to convert path.info file from PATHSAMPLE and AMBER9 into path_all.xyz
- extractedmin2pdb.py: A python program to convert exctractedmin file from PATHSAMPLE and AMBER9 to PDB file
Useful linux stuff
- basic linux commands everyone should know!
- setting up aliases to quickly log you in to a different machine
- transfering 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
- conversion between different data file formats