VMD is a powerful molecular visualization program used for displaying proteins and other molecule files obtained through using programs like gromacs and NAMD.

The use of this program requires the installation of a X-server, either via Linux, Xwin or Mac OS X.

Once installed, using VMD requires two steps:

1. Asking for an interactive node with terminal tunneling

    qsub -I -X

Wait until you are logged in into one of the compute nodes.

2. Running VMD

    module load vmd
    vmd

VMD tutorial and documentation are available in on ITS/HPCC wiki.