Difference between revisions of "Wales Group"
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| + | ===THE WALES GROUP PAGES HAVE MOVED!=== |
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| − | [[Image:Walesgroup1.jpg|thumb|The usual suspects at Byron's Pool after Vanessa's viva|400px|right]] |
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| + | http://www-wales.ch.cam.ac.uk/groupwiki |
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| − | Members: |
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| + | Please bare with us as we move things across. If you notice anything missing, please let me know! |
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| − | * Dr David J. Wales |
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| + | --[[User:csw34|csw34]] 22:04, 19 July 2010 (BST) |
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| − | * Szilard Fejer |
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| − | * Chris Whittleston |
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| − | * Hayley McKay |
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| − | * Dr Joanne Carr |
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| − | * Dr Dwaipayan Chakrabarti |
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| − | * Dr Edyta Malolepsza |
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| − | * Dr Birgit Strodel |
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| − | |||
| − | 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! |
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| − | == Group software == |
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| − | The official documentation can be found [http://www-wales.ch.cam.ac.uk/software.html 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. |
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| − | 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. |
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| − | * [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling. |
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| − | * [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways |
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| − | * [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis |
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| − | == Useful software == |
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| − | |||
| − | * [[CHARMM]] |
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| − | * [[AMBER]] |
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| − | * [[REX (Replica EXchange MD) with the MMTSB-toolset]] |
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| − | * [[gnuplot]] |
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| − | * [[VMD]] |
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| − | * [[Pymol]] |
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| − | * [[xmgrace]] |
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| − | * [[xfig]] |
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| − | * [[disconnectionDPS]] |
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| − | == Useful scripts == |
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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. |
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| − | * [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]]. |
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| − | * [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :) |
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| − | * [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz'' |
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| − | * [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format |
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| − | * [[makerestart]]: A bash script to automatically set up a GMIN restart run |
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| − | * [[recommended bash aliases]] |
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| − | * [[David's .vimrc file]] |
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| − | * [[David's .inputrc file]] |
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| − | |||
| − | == Useful linux stuff == |
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| − | * [[basic linux commands everyone should know!]] |
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| − | * [[piping and redirecting output from one command or file to another]] - how to save yourself hours! |
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| − | * [[setting up aliases to quickly log you in to a different machine]] |
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| − | * [[transfering files to and from your workstation]] -using ''scp'' or ''rsync'' |
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| − | * [[printing files from the command line using 'lpr']] |
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| − | * [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!) |
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| − | * [[the many uses of 'rm' - getting rid of your files safely]] |
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| − | * [[removing an excessive number of files from a directory - when 'rm' just isn't enough]] |
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| − | * [[short 'sed' examples]] |
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| − | * [[short 'awk' examples]] |
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| − | * [[using tar and gzip to compress/uncompress files]] |
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| − | * [[conversion between different data file formats]] -'almost one-line' scripts |
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| − | * [[conversion between different image file formats]] - the ''convert'' command |
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| − | * [[submitting jobs, interactively or to a cluster queue system]] |
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| − | * [[running programs in the background]] - so you can use your shell for other things at the same time |
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| − | == Group practice == |
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| − | 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. |
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| − | * [[Wales Group Conventions when using LaTex | conventions when using LaTex]] |
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| − | * [[Wales Group Fortran conventions for group software | Fortran conventions for group software]] |
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| − | * [[Wales Group Version control | version control ]] |
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Latest revision as of 00:28, 21 July 2010
THE WALES GROUP PAGES HAVE MOVED!
http://www-wales.ch.cam.ac.uk/groupwiki
Please bare with us as we move things across. If you notice anything missing, please let me know! --csw34 22:04, 19 July 2010 (BST)