Gromacs

VMD

    Visual Molecular Dynamics (VMD) is a superb, professional-quality award-winning molecule visualization package freely available for a wide variety of platforms. Full manuals and tutorial material are available from that link.

    It can read a variety of GROMACS-compatible file formats, including .pdb, .gro, .g96, .xtc, and .trr, as well as many others. It cannot read .top or .tpr files.

    VMD and coarse-grained simulations

    Since the default VMD bond-length heuristics are too short for coarse-grained simulations, and VMD does not read GROMACS .tpr run input files another solution is required. The coarse_grain.tcl script from Nicholas Sapay will help with this. Alternatively, the Martini-specific top2psf.pl from Justin Lemkul is also available.

    Could VMD be used as a front end for GROMACS?

    Indeed, yes. VMD includes a Tcl scripting language that seems to allow you to do anything a good scripting language can do, and seems to have good access to the innards of the molecules being displayed. There are numerous VMD front-ends and helper scripts for other computational chemistry tools. It already reads and writes various of the GROMACS file types, but not a .top file or .tpr file, which might be one of the first things one would want to add to the source code (rather than put in script).

    I assume that one could do system calls from Tcl, and just run pdb2gmx and grompp. --Spoel 17:38, 3 July 2007 (CEST)
    Indeed, you could... in fact a editconf and/or gmxdump combo from the script probably obviates any need to parse a .tpr file, except that VMD will read CHARMM/NAMD .psf files and then read a trajectory in and show it using the simulation topology. This is part of why we get beginners complaining about missing bonds, etc. The ability to just read the coordinates and bonding connectivity in a .tpr file to mimic this would be a boon. While someone's there, the charges... :-) --Mabraham 02:09, 4 July 2007 (CEST)

    It is quite simple to parse the output of gmxdump using TCL and to set the bonds in VMD. I did this already to visualize the bonds in the coarse-grained structures and it works very well. VMD is also probably the best known program, which almost everybody use, so it seems to be the best choice for GUI development. Another advantage is the simplicity of TCL and Tk in comparison with C.--Yesint 10:54, 26 September 2007 (CEST)

    Page last modified 22:54, 20 Oct 2009 by mabraham