VMD

Visual Molecular Dynamics is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
It is useful to visualise trajectories.

The home page is: https://www.ks.uiuc.edu/Research/vmd/.

It is available on Aurora:
module load vmd/1.9.2


Simple use with Amber simulations

  1. Start VMD:
    vmd
  2. File - New molecule
  3. Enter the prmtop file as the file name
    and AMBER7 Parm as the file type
  4. Load next a trajectory with the file type AMBER coordinates
  5. In VMD Main, click on
    Graphics - Representations - Create Rep
    Here you can select a molecule
    resname L01
    or a surrounding
    all and within 6 of resname L01