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 no 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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| − | * [[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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| − | * [[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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| − | == Useful linux stuff == |
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| − | * [[basic linux commands everyone should know!]] |
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| − | * [[setting up aliases to quickly log you in to a different machine]] |
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| − | * [[using 'scp' to transfer files to and from your workstation]] |
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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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| − | * [[data manipulation using 'sed']] |
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| − | * [[data manipulation using 'awk']] |
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| − | * [[using tar and gzip to compress/uncompress files]] |
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| − | == Group practice == |
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| − | * [[conventions when using LaTex]] |
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| − | * [[Fortran conventions for group software]] |
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Latest revision as of 23:28, 20 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)