User contributions for Adk44

12:1812:18, 13 May 2019 diff hist +587‎ N David's .inputrc file ‎ Created page with "This will reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and backward search in history matching the start of what you have alr..." current
12:1712:17, 13 May 2019 diff hist +1,116‎ N Recommended bash aliases ‎ Created page with "~wales/.bashalias Copying ~wales/.inputrc to your home directory will also reduce your typing. It sets up ESC then . as the last item on the previous line and ESC then , and..." current
12:1712:17, 13 May 2019 diff hist +1,658‎ N Pdb to movie.py ‎ Created page with " #! /usr/bin/env python """ Calculates the movieseg or a OPTIM coord file from a given PDB file arguments: 50 format('CA: ',3(f8.3,1x),'CB: ',3(f8..." current
12:1612:16, 13 May 2019 diff hist +996‎ N Colourdiscon.py ‎ Created page with "Script useful for DISCONNECTIVITY users To do this save the code in ''colourdiscon.py'' file, change privileges of this file: chmod 755 colourdiscon.py and type: ./Colou..." current
11:1611:16, 13 May 2019 diff hist +4,201‎ N Local rigid body in OPTIM ‎ Created page with "Here we describe our implementation of local rigid body in OPTIM. ---- POTENTIAL ---- Currently I have only done this for CHARMM and NAB only. ---- MAKEIMAGE ---- Currently..." current
11:1611:16, 13 May 2019 diff hist +3,260‎ N Local Rigid Body Framework ‎ Created page with "== Introduction == In this framework you can group arbitrary sets of atoms into rigid bodies. It currently works only in GMIN, but I will soon implement this in OPTIM too. You..." current
11:1611:16, 13 May 2019 diff hist +20,574‎ N Rigid body input files for proteins using genrigid-input.py ‎ Created page with "== Overview == The use of rigid bodies requires two files: the rbodyconfig file (definition of rigid bodies) and the coordsinirigid file. The genrigid-input.py creates those f..." current
11:1511:15, 13 May 2019 diff hist +1,682‎ N Automatic Rigid Body Grouping ‎ Created page with "== Introduction == For large systems, grouping the rigid bodies can be tedious and painful. I intend to automate this with a pdb file as an input. Unfortunately depending on f..." current
11:1511:15, 13 May 2019 diff hist +3,152‎ N Computing normal modes in angle-axis ‎ Created page with "On this page I will describe how you can compute normal modes in angle-axis framework. It is likely that you may have to implement your own potential (until rigid body sandbox..." current
11:1411:14, 13 May 2019 diff hist +1,040‎ N Angle-axis framework ‎ Created page with "= Introduction = In the angle-axis framework, rotations are described by a vector of rotation, while its magnitude is the angle of rotation. A good review on rotations in gene..." current
11:1411:14, 13 May 2019 diff hist +5,958‎ N GenCoords Models ‎ Created page with "The following parametric models are defined for use with the GenCoords program. The parameters listed here are specified at run time as param1, param2, ..., paramNp in an..." current
11:1311:13, 13 May 2019 diff hist +2,149‎ N GenCoords ‎ Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
11:1311:13, 13 May 2019 diff hist +1,853‎ N Gencoords ‎ Created page with "GenCoords is a Fortran program to generate arbitrary arrangements of ellipsoids interacting with the paramonov-yaliraki potential. A series of user defined parametric mode..." current
11:1311:13, 13 May 2019 diff hist +1,544‎ N Ellipsoid.xyz ‎ Created page with "The ellipsoid.xyz file is the output of GMIN when using the PY keyword. The file defines the positions and orientations of the set of ''repulsive'' ellipsoids for each [..." current
11:1211:12, 13 May 2019 diff hist +37‎ N Ellipsoid.model.xyz ‎ Created page with "Same as the ellipsoid.xyz format." current
11:1111:11, 13 May 2019 diff hist +899‎ N Ellipsoid.model ‎ Created page with "The ellipsoid.model file is used to specify the parametric model that GenCoords uses to arrange a set of ellipsoids in a starting pattern. The file has the following forma..." current
11:1111:11, 13 May 2019 diff hist +2,664‎ N Density of states and thermodynamics from energy distributions at different temperatures ‎ Created page with "This is a tutorial for a set of MATLAB scripts which takes as input potential energy values observed for different replicas in a temperature Replica Exchange (REX) simulation..." current
11:1011:10, 13 May 2019 diff hist +710‎ N Xmgrace ‎ Created page with "The below command will read in a saved session file, read some data in column format (blank space delimited). Use the index and the second column as the X and Y axises. A pos..." current
11:1011:10, 13 May 2019 diff hist +638‎ N Xmakemol ‎ Created page with "A program for visualizing atomic and molecular systems. It is fast and flexible enough to view clusters, and bioploymers The input format has one atom per line with an atom i..." current
11:0911:09, 13 May 2019 diff hist +2,147‎ N Xfig ‎ Created page with "<h2>LaTeX fonts in Xfig figures</h2> Xfig supports LaTex fonts. Fig files are thus a convenient intermediate file format when generating figures for LaTeX documents. <h3>Man..." current
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

User contributions for Adk44

13 May 2019

Navigation menu

Search