VMD

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. 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 coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

The complete set of features can be found here.

Installations on NSC systems

Tetralith and Sigma

VMD is available via the module system on Tetralith and Sigma. For more information about available versions, please see the Tetralith and Sigma Software list.

How to use

Access to the VMD binary is given via the module system, e.g. do a

module load vmd/1.9.3-nsc1

and then issue the “vmd” command. Remember that you will need to be logged in with X forwarding or Thinlinc to make use of the interface. NSC recommends launching VMD using ‘vglrun’ in a Thinlinc session:

vglrun vmd