Gromacs

Visualization Software

    Some programs that are useful for visualizing either a trajectory file and/or a coordinate file are:

    • VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Reads GROMACS trajectories.
    • PyMOL - capable molecular viewer with support for animations, high-quality rendering, crystallography, and other common molecular graphics activities. Does not read GROMACS trajectories in default configuration, requiring conversion to PDB or similar format. When compiled with vmd plugins, trr & xtc files can be loaded.
    • gOpenMol - small molecules, and to lesser extent protein structures, as well as the chemical properties, total electron densities and molecule orbitals of small molecules can be visualized and analyzed.
    • Rasmol - the derivative software "Protein Explorer" (below) might be a better alternative, but the Chime component requires windows. Rasmol works fine on Unix.
    • Protein Explorer - a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. It runs on Windows or Macintosh/PPC computers.
    • Chimera - A full featured, Python-based visualization program with all sorts of features for use on any platform. The current version reads gromacs trajectories.
    • Molscript - This is a script-driven program form high-quality display of molecular 3D structures in both schematic and detailed representations. You can get an academic license for free from Avatar.

    Also if appropriate libraries were found at configure-time, gmx view can useful.

     

    Topology bonds vs Rendered bonds

    Remember that each of these visualization tools is only looking at the coordinate file you gave it (except when you give gmx view a .tpr file). Thus it's not using your topology which is described in either your .top file or your .tpr file. Each of these programs makes their own guesses about where the chemical bonds are for rendering purposes, so do not be surprised if the heuristics do not always match your topology. Apply your brain, here!

     

    Page last modified 07:18, 8 Feb 2016 by mabraham