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    Linked below are programs written by GROMACS users to carry out a variety of functions.  They are not necessarily tested or verified by the GROMACS developers.

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     spacer ambconv.tgz
    Converts AMBER topology and coordinate files to GROMACS format. Perturbation calculations are supported. Experimental support of TINKER format. Tested on numerous molecules (incl. DNA hexamer with ligand) with energy difference between AMBER and GROMACS less than 0.01%. Uploaded 02:59 November 30, 2002 by Filip Ryjacek (ryjacek@msn.com)
    		34.19 kB17:07, 23 May 2009rossenActions
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     spacer analyse.pl
    Moved from Joomla, there were no comments about this file.
    		1511 bytes11:11, 23 May 2009rossenActions
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     spacer Calc_Entropies.tgz
    This script calculates the entropies from the output of g_covar by applying the quasiharmonic approximation. See details inside. Was tested on GMX 3.2.1 only. A script for GMX 3.1.4 is available from the author.
    		13.73 kB17:07, 23 May 2009rossenActions
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     spacer chandran.tgz
    Chandran is a tool to make a ramachandran plot colored by occupancy. It reads rama.xvg and produces rama.xpm which can be converted to ps with xpm2ps. Uploaded 12:29 October 09, 2002 by Marcos Villarreal (arloa@dqb.fcq.unc.edu.ar)
    		52.82 kB17:06, 23 May 2009rossenActions
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     spacer charmm2gromacs-pvm.py
    A script to convert charmm topology files to gromacs. It has been tested recently with CGenFF files and seems to work. Check the output carefully before using.
    		30.31 kB15:08, 15 Oct 2012spoelActions
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     spacer charmm_to_gromacs.tgz
    Two perl scripts intended to facilitate calculations using GROMACS programs and CHARMM forcefields. These are both considered alpha-release - users should verify the accuracy of their performance by comparing energy evaluations on the same structures in CHARMM and GROMACS. convert_charmm_to_gromacs.pl takes a CHARMM force field file as input and produces ffcharmmbon.itp and ffcharmmnb.itp which when placed in the GMXLIB directory allow pdb2gmx to accept a "-ff charmm" flag and produce an approximation to a CHARMM .top file. This approximation is not normally useful, because pdb2gmx does not natively create Urey-Bradley interactions where they are used by CHARMM, nor does it readily use the 1-4 LJ parameters that differ from the normal LJ parameters for some atom types, nor can it generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion. fix_top_for_charmm.pl takes the .top file produced by pdb2gmx, runs grompp on it and notices each occurence of the above three types of error and fixes them, outputing a new .top file that the user can keep and use themselves as input to grompp at their convenience. The advantage of making available the conversion program, rather than the just the results is that it will be easy to use convert different versions of CHARMM force fields, or modified versions so long as the .prm format stays the same. Also my algorithms can be checked, and corrected if necessary. No attempt is made to convert the CHARMM residue toplogies - please consult those of Yuguang Mu at www.gromacs.org/old/topologies/uploaded_force_fields/charmm_gromacs.tar.gz in the first instance. Both scripts are released under the GNU General Public License.
    		13.82 kB17:06, 23 May 2009rossenActions
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     spacer cmd_make_ndx.tgz
    This scripts takes an alignment in FASTA format and generates comands for make_ndx. the ndx files created with that commands allows g_confrms to superimpose the structures corresponding to the aligned sequences, even if they don't have the same number of aminoacids (only the aligned aminoacids in the FASTA file will be superimposed)
    		2.12 kB17:05, 23 May 2009rossenActions
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     spacer ConvertGromos2Gromacs.tgz
    This is a program to convert GROMOS96 formatted topology, and conformation files to their GROMACS equivalents. Uploaded 19:41 January 10, 2003 by Claudio M. Soares (claudio@itqb.unl.pt)
    		27.83 kB17:05, 23 May 2009rossenActions
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     spacer demo.patch.not.gzipped.gz
    Solaris\' csh has trouble with exclamation points at the end of strings; this patch removes the troublesome !\'s in the gromacs demo. Uploaded 04:33 April 15, 2002 by Nathan Sharfi (nisharfi@csupomona.edu)
    		1416 bytes11:34, 23 May 2009rossenActions
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     spacer do_multiprot_dist.tgz
    do_multiprot reads a trajectory file and aligns it to a reference structure each time frame calling the multiprot program. This allows you to use a reference structure whose sequence is different than that of the protein in the trajectory, since the alignment is based on the geometry, not sequence. The output of do_multiprot includes the rmsd and the number of residues on which it was calculated. To use do_multiprot, you must have the multiprot program itself. For information about multiprot (and how to get it), see: bioinfo3d.cs.tau.ac.il/MultiProt to use do_multiprot 1. Unpack archive tar -xzvf do_multiprot.tgz this yield the directory do_multiprot_dist You must also make sure that you have gromacs and multiprot installed. 2. >cd [location] where location is the full path to do_multiprot_src directory 3. get the information from the README and INSTALL files
    		1185.01 kB17:02, 23 May 2009rossenActions
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     spacer dock41.tar
    dock is a Perl script to perform MD simulations with Gromacs in different flavours. Specially designed to study Proteins and Protein/Ligand interactions, it automates several common steps like Energy Minimization and Position Restraints before MD step. In addition, it is able to restart a simulation after a crash in a very easy way. Files are organized in subdirectories separating data files from result files and using uniform file names. In addition, it can deal with PRODRG topology files allowing the study of complexes between proteins and arbitrary ligands.
    		1620 kB17:05, 23 May 2009rossenActions
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     spacer ego2xtc.tar.gz
    ego2xtc will convert trajectories generated by the EGO simulation software (multiple .ego files) to the .xtc trajectory format. This allows EGO trajectories to be analysed by the gromacs analysis and trajectory conversion tools AND saves a large amount of disk space. (package contains both source code and binaries for DEC, SGI and linux) Uploaded 08:49 December 02, 2002 by Bert de Groot (bgroot@gwdg.de)
    		125.03 kB17:02, 23 May 2009rossenActions
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     spacer g_covar.tgz
    General Information: ------------------- This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation > 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions.
    		1569.75 kB11:38, 23 May 2009rossenActions
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     spacer G_DESORT.tgz
    Using the -sort option to mdrun greatly increases scaling efficiency (100% to 4cpu). g_desort is then required to deshuffle and desort the trajectory file, thereby recovering full trajectory information. This is not recommended for beginner gromacs users. Users are encouraged to test their results before committing to long runs.
    		4.79 kB11:38, 23 May 2009rossenActions
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     spacer g_puckering_gmx3_3_x.tgz
    g_puckering computes the Cremer-Pople-Puckeing Parameters of Pyranoses and Hexanoses. Homepage: oc24.uni-paderborn.de/~revilo/en/g_puckering.html - Version for Gromacs 3.3.x
    		22.24 kB19:16, 20 Oct 2009revilo?Actions
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     spacer g_puckering_gmx4_0_x.tgz
    g_puckering computes the Cremer-Pople-Puckeing Parameters of Pyranoses and Hexanoses. Homepage: oc24.uni-paderborn.de/~revilo/en/g_puckering.html - Version for Gromacs 4.0.x
    		22.23 kB19:16, 20 Oct 2009revilo?Actions
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     spacer g_rdf-com.c
    This is a program to calculate the rdf with COM. This program is based on the original of the g_rdf.c and the work of Jochen Hub. As default, the structure center is calculated. One can calculate the center of mass by opening line 394 and closing line 393. The -com_rdf -o and the -com_rdf -cn are tested. If one wants to calculate other parameters, please use the original g_rdf.c.
    		37.65 kB11:11, 23 May 2009rossenActions
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     spacer g_sdf.c.gz
    g_sdf calculates the spatial distribution function (SDF) of a set of atoms relative to a reference molecule. Output is aN isosurface file in plt format, readable by gOpenMol and VMD. Written by Christoph Freudenberger, with modification by Tsjerk Wassenaar to work with 3.3.1.
    		6.68 kB11:36, 23 May 2009rossenActions
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     spacer g_spatial.tar.gz
    g_spatial calculates the spatial distribution function and outputs it in a form that can be read by VMD as Gaussian98 cube format. This program differs from g_sdf in that it gives the user full control of the alignment procedure. The downside is that it requires more time and more disk space.
    		5.53 kB11:36, 23 May 2009rossenActions
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     spacer gd.tgz
    Here is a script that will run a Galactic dynamics simulation. The system provides 1 black (darjk grey) hole, some stars, some planets and some comets, all under the influence of gravity only. Please hack the script as you like. You will need the latest CVS version of GROMACS (from today!) in order to bypass a check in grompp for negative epsilon_r. If you ish you can also comment out the check in readir.c, it will not influence your normal simulations.
    		1881 bytes17:07, 23 May 2009rossen
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