VMD is a molecular visualisation program for displaying, animating, and analysing large biomolecular systems using 3-D graphics and built-in scripting. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and colouring a molecule. VMD can be used to animate and analyse the trajectory of a molecular dynamics (MD) simulation.
Launching VMD on Setonix Remote Visualisation
First, start a remote desktop session and launch a terminal. For details on how to do this, see Getting Started With Setonix Remote Visualisation.
Then, run the following commands to launch VMD:
module load virtualgl/3.1 vmd/1.9.3 vglrun vmd
After executing these commands, the VMD application windows will open:
