User contributions for Adk44

13 May 2019

• 11:0911:09, 13 May 2019 diff hist 0‎ N File:VmdAnnotate.jpg ‎No edit summary current
• 11:0911:09, 13 May 2019 diff hist +8,489‎ N VMD script to annotate each frame of a trajectory ‎ Created page with "'''annotateTraj.tcl''' contains procedures to annotate each frame of a pdb trajectory file with data from the pdb file (e.g. energy from the header line of each frame) or comp..." current
• 11:0811:08, 13 May 2019 diff hist +762‎ N PlotGMINms.tcl ‎ Created page with "The plotGMINms function is a script to plot out ellipsoid.xyz files which are the output from GMIN when using the PY potential keyword or GenCoords when generating..." current
• 11:0811:08, 13 May 2019 diff hist +658‎ N Useful .vmdrc file ‎ Created page with "VMD has some useful features, but also a number of irritating startup options. Fortunately VMD is highly configurable. Add the following in a file calle .vmdrc for improved (..." current
• 11:0711:07, 13 May 2019 diff hist +2,706‎ N Path2xyz.py ‎ Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be converted to xyz format using Python program presented below. To do this save the code in ''path2xyz.py'' fi..." current
• 11:0011:00, 13 May 2019 diff hist +1,102‎ N Loading coordinate files into VMD with the help of an AMBER topology file ‎ Created page with "AMBER topology files have a lot more information in them than simple .pdbs so sometimes it's really useful to be able to load them in directly, for example when you want to lo..." current
• 10:5910:59, 13 May 2019 diff hist 0‎ N File:Molefacture.png ‎No edit summary current
• 10:5910:59, 13 May 2019 diff hist +3,326‎ N Using VMD to display and manipulate '.pdb' files ‎ Created page with "VMD's default input format is pdb and so it isn't necessary to specify a file extension if loading from the command line, so the following syntax could be used to load several..." current
• 10:5810:58, 13 May 2019 diff hist +1,768‎ N VMD ‎ Created page with "VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug..."
• 10:5810:58, 13 May 2019 diff hist +2,732‎ N Extractedmin2pdb.py ‎ Created page with "Program useful for AMBER9 and NAB users If you extracted minima from ''points.min'' file and you have ''extractedmin'' file you can use Python program presented below to con..." current
• 10:5810:58, 13 May 2019 diff hist +3,511‎ N Path2pdb.py ‎ Created page with "Script useful for AMBER9 and NAB users ''path.info'' file can be easy converted to the PDB format using Python program presented below. PDB file can be loaded to VMD and you..." current
• 10:5710:57, 13 May 2019 diff hist +3,310‎ N Advanced colouring ‎ Created page with "You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.o..." current
• 10:5710:57, 13 May 2019 diff hist 0‎ N File:Ray2.png ‎No edit summary current
• 10:5610:56, 13 May 2019 diff hist 0‎ N File:Ray1.png ‎No edit summary current
• 10:5610:56, 13 May 2019 diff hist +5,214‎ N Producing sexy ray-traced images ‎ Created page with "Pardon the title but you'll understand when you see the results! === Before you ray trace === Before you start playing with ray tracing, you need to be sure that you're happy..." current
• 10:5510:55, 13 May 2019 diff hist +1,102‎ N Loading AMBER prmtop and inpcrd files into Pymol ‎ Created page with "AMBER topology files have a lot more information in them than simple .pdbs so sometimes it's really useful to be able to load them in directly, for example when you want to lo..." current
• 10:5510:55, 13 May 2019 diff hist +1,668‎ N Pymol ‎ Created page with "Pymol is an open-source molecular visualisation program (binaries, full documentation are not freely available, however). Compilation of v1.1 is straightforward (v1.2 is in b..." current
• 10:5410:54, 13 May 2019 diff hist +769‎ N Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays ‎ Created page with "GMIN jobs on large systems (e.g. 5000 LJ atoms) can sometimes fail with memory allocation errors like this one: 0: ALLOCATE: 18446744071814864320 bytes requested; not enoug..." current
• 10:5410:54, 13 May 2019 diff hist +1,723‎ N Pgprof ‎ Created page with "Profiling an executable can give useful information on where particular calculations spend the majority of their time, so that you can go for the big win in terms of recoding..." current
• 10:5310:53, 13 May 2019 diff hist +6,320‎ N Simulations using OPEP ‎ Created page with "=== Why you might want to use OPEP === OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly..." current
• 10:5310:53, 13 May 2019 diff hist +1,047‎ N REX (Replica EXchange MD) with the MMTSB-toolset ‎ Created page with "The MMTSB Toolset is a group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD (both constant temperature and replica exchange..." current
• 10:5210:52, 13 May 2019 diff hist +676‎ N Installing and setting up the MMTSB toolset ‎ Created page with "The latest version (Sep 2011) of MMTSB [http://mmtsb.org] is installed in /home/ss2029/SWins/mmtsb_toolset on CLUST. To use it set the following variables in your .bashrc: <..." current
• 10:4010:40, 13 May 2019 diff hist +1,047‎ N MMTSB-toolset ‎ Created page with "The MMTSB Toolset is a group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD (both constant temperature and replica exchange..." current
• 10:3910:39, 13 May 2019 diff hist +3,350‎ N Latex2html ‎ Created page with "The latex2html script takes a latex document, and turns it into an equivalent set of HTML pages - broken down by section and then subsection. It generates an index.html page l..." current
• 10:3810:38, 13 May 2019 diff hist +2,614‎ N Installing GROMACS on Clust ‎ Created page with "* Download GMX (gromacs-4.5.4.tar.gz [http://www.gromacs.org/Downloads]) and FFTW ( fftw-3.2.2.tar.gz [http://www.fftw.org/download.html]) source codes and extract in ~/SW..." current
• 10:3810:38, 13 May 2019 diff hist +827‎ N Linear and non-linear regression in gnuplot ‎ Created page with "You can fit a simple linear regression to a set of data quickly using gnuplot: <pre> # Fit a linear polynomial to the data. # These are the primary instructions for linear re..." current
• 10:3710:37, 13 May 2019 diff hist +675‎ N Plotting data in real time ‎ Created page with "If your code produces output in real time during a run, it can be both informative and interesting to be able to view the results as they come in. This can be done simply usin..." current
• 10:3710:37, 13 May 2019 diff hist +2,280‎ N Plotting a quick histogram in gnuplot using the raw data ‎ Created page with "You can use the below script to plot a quick and dirty histogram of your data. There are three methods here, only method 1 is uncommented. The only variables you need to set a..." current
• 10:3610:36, 13 May 2019 diff hist +718‎ N Gnuplot ‎ Created page with "gnuplot is an open source graphing program. The homepage is located [http://www.gnuplot.info/ here] and has full documentation. It is often very difficult to find useful comma..." current
• 10:3510:35, 13 May 2019 diff hist +2,786‎ N DMACRYS interface ‎ Created page with "== The interface == The current idea of the interface is to use the dmacrys main code (routine CASCAD) to parse the input files and initialize all variables. At the point the..." current
• 10:3510:35, 13 May 2019 diff hist +3,371‎ N Constructing Free Energy Disconnectivity Graphs ‎ Created page with "This is a short summary of how you can construct a free energy disconnectivity graph from a potential energy stationary point database. '''To start off you will need the fol..." current
• 10:3410:34, 13 May 2019 diff hist +2,569‎ N If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing) ‎ Created page with "Making a charmm19 .crd file from an experimental PDB structure is not so straightforward, I've found. The same can be true if the PDB file has missing atoms. Apart from charm..." current
• 10:3310:33, 13 May 2019 diff hist +11,790‎ N Calculating order parameters ‎ Created page with "When constructing a potential/free energy surface, or trying to understand the landscape topology by colouring a disconnectivity graph, you need to calculate order parameters..." current
• 10:3310:33, 13 May 2019 diff hist +3,684‎ N Calculating molecular properties ‎ Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..." current
• 10:3210:32, 13 May 2019 diff hist +3,836‎ N Calculating energy of a conformation ‎ Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..." current
• 10:3210:32, 13 May 2019 diff hist +2,443‎ N Converting between '.crd' and '.pdb' ‎ Created page with "You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the conversion between different data file f..." current
• 10:3110:31, 13 May 2019 diff hist +14,527‎ N Generating pdb, crd and psf for a peptide sequence ‎ Created page with "Top level: CHARMM Below script does for CHARMM what Leap does for AMBER (see Setting_up) -- generates input files given a peptide sequence. Here, it generates struc..." current
• 10:3010:30, 13 May 2019 diff hist +3,711‎ N CPMDInput ‎ Created page with "The following options for the local CPMD code are in addition to the options given in the manual for CPMD v3.11.1. Please keep any changes to this page up-to-date with the LO..." current
• 10:3010:30, 13 May 2019 diff hist +2,455‎ N CamCASP/CodeExamples/DirectAccess ‎ Created page with "<pre> program directaccess !Write a direct access file and read it. !Written with the hope of tracing a bug in gfortran - if it is a bug! implicit none integer, parameter ::..." current
• 10:3010:30, 13 May 2019 diff hist +633‎ N CamCASP/ToDo/Memory ‎ Created page with "CamCASP => ToDo => Memory == Memory == What are the large objects in the code and what do we do about them? # Non-DF Hessians: o^2 v^2 # TAO, TMO..." current
• 10:2910:29, 13 May 2019 diff hist +3,785‎ N CamCASP/ToDo/diskIO ‎ Created page with "CamCASP => ToDo => Disk I/O == Disk I/O == We currently spend a '''lot''' of time in disk I/O. Three years ago the situation was not so bad: we us..." current
• 10:2910:29, 13 May 2019 diff hist +493‎ N CamCASP/Bugs ‎ Created page with "CamCASP => Bugs ==CamCASP Bugs== 7. Incorrect behaviour of polarizabilities 6. Rotation bugs 5. CamCASP/Bugs/5|GA..." current
• 10:2810:28, 13 May 2019 diff hist +453‎ N CamCASP/Notes ‎ Created page with "CamCASP => Notes ==Notes on CamCASP usage== * Rotating integrals * Energy Scans with CamCASP * CamCASP/Notes/3 | E..." current
• 10:2810:28, 13 May 2019 diff hist +1,138‎ N CamCASP/Programming/5/example1 ‎ Created page with "CamCASP => Programming => Auxiliary Basis sets Example 1 Input file <pre> Title DF and integral tests: 1s1p basis..." current
• 10:2710:27, 13 May 2019 diff hist +533‎ N CamCASP/Programming ‎ Created page with "CamCASP => Programming == Programmers Notes == * Status * Basis functions * CamCASP/Programming/2 | The..." current
• 09:3209:32, 13 May 2019 diff hist +180‎ N CamCasp ‎ Created page with "Bugs http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/CamCasp/Bugs To Do http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/CamCasp/ToDo --ajs1 14:45, 20 October 2008..." current
• 09:3209:32, 13 May 2019 diff hist +1,588‎ N Aux2bib ‎ Created page with "'''aux2bib''' is part of the bibtools package, which you can obtain [https://ctan.org/pkg/bibtools here]. As you might be able to guess from the name, it takes a .aux file fro..." current
• 09:3109:31, 13 May 2019 diff hist +2,753‎ N Perm-prmtop.py ‎ Created page with "'''What is it and why is it important?''' We have noticed that the AMBER9 potential is not symmetric with respect to permutations of identical atoms e.g. hydrogen atoms in th..." current
• 09:3109:31, 13 May 2019 diff hist +5,610‎ N Performing a hydrogen-bond analysis ‎ Created page with "An analysis of the hydrogen-bonding network can provide useful structural information in many situations. For example, it can be used to classify minima (and hence colour disc..." current
• 09:3009:30, 13 May 2019 diff hist +12,903‎ N REMD with AMBER ‎ Created page with "===Setting up AMBER REX=== To run REMD with AMBER you need '''sander.MPI'''. You can either copy it (clust:~bs360/bin/sander.MPI) or create your own. To do so you have to cop..." current