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.
Starting a VMD session:
Please follow the instructions at Getting started: Web-based remote visualisation 7/4/2020 and start either a "Desktop" or "Xterm" session. If you have started a "Desktop" session, open a Xterm terminal by right clicking on the desktop.
Inside your Xterm window, type the following commands: