Wales Group - Revision history

import>Csw34 at 23:28, 20 July 2010

2010-07-20T23:28:14Z

← Older revision		Revision as of 23:28, 20 July 2010
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	Please bare with us as we move things across. If you notice anything missing, please let me know!		Please bare with us as we move things across. If you notice anything missing, please let me know!
	--[[User:csw34\|csw34]] 22:04, 19 July 2010 (BST)		--[[User:csw34\|csw34]] 22:04, 19 July 2010 (BST)


	Math environment test:

	<math>\alpha^2+\beta^2=1</math>

import>Csw34 at 18:25, 20 July 2010

2010-07-20T18:25:48Z

← Older revision		Revision as of 18:25, 20 July 2010
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	Please bare with us as we move things across. If you notice anything missing, please let me know!		Please bare with us as we move things across. If you notice anything missing, please let me know!
	--[[User:csw34\|csw34]] 22:04, 19 July 2010 (BST)		--[[User:csw34\|csw34]] 22:04, 19 July 2010 (BST)


			Math environment test:

			<math>\alpha^2+\beta^2=1</math>

import>Csw34 at 21:04, 19 July 2010

2010-07-19T21:04:27Z

← Older revision		Revision as of 21:04, 19 July 2010
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	http://www-wales.ch.cam.ac.uk/groupwiki		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!
			--[[User:csw34\|csw34]] 22:04, 19 July 2010 (BST)

import>Csw34 at 21:03, 19 July 2010

2010-07-19T21:03:17Z

← Older revision		Revision as of 21:03, 19 July 2010
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			===THE WALES GROUP PAGES HAVE MOVED!===
	[[Image:Walesgroup1.jpg\|thumb\|The usual suspects at Byron's Pool after Vanessa's viva\|400px\|right]]
	[[Image:Mikebats-small.png\|thumb\|Mike bringing American passion to English sport. It's just not Cricket!\|200px\|right]]
	Members:

			http://www-wales.ch.cam.ac.uk/groupwiki
	* Prof David J. Wales
	* Chris Whittleston
	* Hayley McKay
	* Oleksandr Poplavskyy
	* Marianne Bauer
	* Dr Livia Bartok-Partay
	* Dr Joanne Carr
	* Dr Dwaipayan Chakrabarti
	* Dr Edyta Malolepsza
	* Dr Birgit Strodel
	* Dr Szilard Fejer
	* Dr Jason Green
	* Dr Erwin Lijnen
	with
	* Celebrity batsman, Dr Mike Prentiss

	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 ==
	Our software is managed under Subversion (SVN) version control. For information on how to set up your SVN details and access the code, see the [[SVN setup]] page. Tips on good practice when using SVN can be found on the group [[Wales Group Version control \| version control ]] page. It is highly recommended that you read this once you have set up your details. Once you're up and running, you should definitely take a look at the Theory Sector [[SVN Page]] which is chock full of useful info on the commands you'll be using on a regular basis.

	The official documentation can be found [http://www-wales.ch.cam.ac.uk/software.html here]. It is highly recommended 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. The below links provide more information on each piece of code, including worked tutorials and general help!

	* [[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]]
	* [[latex2html]]
	* [[aux2bib]] - to generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
	* [[xfig]]
	* [[disconnectionDPS]]
	* [[Xmakemol]]
	* [[GAMESS]]

	== 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
	* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
	* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
	* [[makerestart]]: A bash script to automatically set up a GMIN restart run
	* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
	* [[recommended bash aliases]]
	* [[David's .vimrc file]]
	* [[David's .inputrc file]]
	* [[Useful .vmdrc file]]

	== Useful linux stuff ==

	===Basics===
	* [[basic linux commands everyone should know!]]
	* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!

	===Remote access===
	* [[setting up aliases to quickly log you in to a different machine]]
	* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
	* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
	* [[mounting sharedscratch locally]]

	===Find and replace===
	* [[short 'sed' examples]]
	* [[quick guide to awk]]
	* [[short 'awk' examples]]

	===File manipulation===
	* [[using tar and gzip to compress/uncompress files \| using tar and bzip2 to compress/uncompress files]]
	* [[conversion between different data file formats]] -'almost one-line' scripts
	* [[conversion between different image file formats]] - the ''convert'' command
	* [[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]]

	===Cluster queues===
	* [[submitting jobs, interactively or to a cluster queue system]]
	* [[identifying job on a node]] - if you need to kill only one of few running jobs
	* [[see unpacked nodes]] - if you want to see which nodes aren't currently packed so that you know which ones to submit to

	===Miscellaneous/uncategorised===
	* [[running programs in the background]] - so you can use your shell for other things at the same time
	* [[finding bugs in latex documents that will not compile]]
	* [[printing files from the command line using 'lpr']]

	== 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.

	* [[SVN best practice]] - before you commit anything, make sure you read this!
	* [[Wales group calendars]] - so you always know who is around to help you debug, or when you should not come into work wearing your PJs.
	* [[Adding example input for Wales group programs \| adding example input for your work ]]
	* [[Wales Group Conventions when using LaTex \| conventions when using LaTex]]
	* [[Wales Group Fortran conventions for group software \| Fortran conventions for group software]]
	* [[Wales Group Version control \| version control ]]
	* [[Group wish list]] - would like to see a new feature in GMIN? Can you think of a way to improve things but you're not sure how to do it? Add your thoughts here!
	* [[Chris's 'all you can eat' tips]] - by popular request
	* [[Bug hunting tips for group code]]

import>Op226 at 21:07, 10 May 2010

2010-05-10T21:07:52Z

← Older revision		Revision as of 21:07, 10 May 2010
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	* Chris Whittleston		* Chris Whittleston
	* Hayley McKay		* Hayley McKay
			* Oleksandr Poplavskyy
	* Marianne Bauer		* Marianne Bauer
	* Dr Livia Bartok-Partay		* Dr Livia Bartok-Partay

import>Mp466: /* Useful scripts */

2009-11-30T02:36:52Z

Useful scripts

← Older revision		Revision as of 02:36, 30 November 2009
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	* [[David's .vimrc file]]		* [[David's .vimrc file]]
	* [[David's .inputrc file]]		* [[David's .inputrc file]]
			* [[Useful .vmdrc file]]

	== Useful linux stuff ==		== Useful linux stuff ==

import>Em427 at 14:58, 31 October 2009

2009-10-31T14:58:00Z

← Older revision		Revision as of 14:58, 31 October 2009
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	* Chris Whittleston		* Chris Whittleston
	* Hayley McKay		* Hayley McKay
⚫	* Livia Bartok-Partay
	* Marianne Bauer		* Marianne Bauer
		⚫	* Dr Livia Bartok-Partay
	* Dr Joanne Carr		* Dr Joanne Carr
	* Dr Dwaipayan Chakrabarti		* Dr Dwaipayan Chakrabarti

import>Em427 at 16:28, 29 October 2009

2009-10-29T16:28:05Z

← Older revision		Revision as of 16:28, 29 October 2009
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	* Prof David J. Wales		* Prof David J. Wales
⚫	* Szilard Fejer
	* Chris Whittleston		* Chris Whittleston
	* Hayley McKay		* Hayley McKay
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	* Dr Edyta Malolepsza		* Dr Edyta Malolepsza
	* Dr Birgit Strodel		* Dr Birgit Strodel
		⚫	* Dr Szilard Fejer
	* Dr Jason Green		* Dr Jason Green
	* Dr Erwin Lijnen		* Dr Erwin Lijnen

import>Csw34: /* Group practice */

2009-10-27T11:55:10Z

Group practice

← Older revision		Revision as of 11:55, 27 October 2009
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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.		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.

			* [[SVN best practice]] - before you commit anything, make sure you read this!
	* [[Wales group calendars]] - so you always know who is around to help you debug, or when you should not come into work wearing your PJs.		* [[Wales group calendars]] - so you always know who is around to help you debug, or when you should not come into work wearing your PJs.
	* [[Adding example input for Wales group programs \| adding example input for your work ]]		* [[Adding example input for Wales group programs \| adding example input for your work ]]

import>Khs26: /* Remote access */

2009-10-16T12:53:13Z

Remote access

← Older revision		Revision as of 12:53, 16 October 2009
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	* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''		* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
	* [[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!)
			* [[mounting sharedscratch locally]]

	===Find and replace===		===Find and replace===