Contents


Deprecated: please see new documentation site.



From the VMD project page:

VMD is designed for the 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.

Version Information

Current

  • Version:
    • 1.8.6
  • SoftEnv Name:
    • +vmd-1.8.6
  • Executable:
    • /usr/local/package/vmd-1.8.6/bin/vmd-1.8.6
  • Available on:
    • Bluedawg
    • Neptune

Other Available Versions

  • Version:
    • 1.8.5
  • SoftEnv Name:
    • +vmd-1.8.5
  • Executable:
    • /usr/local/package/vmd-1.8.5/bin/vmd-1.8.5
  • Available on:
    • Bluedawg
    • Neptune

Using VMD Interactively

Login to the head node using the following ssh command

% ssh -X -Y bluedawg.loni.org

Then, execute the command:

 % /usr/local/packages/vmd-1.8.6/bin/vmd-1.8.6

Form more information on X11 forwarding issues, please see X11 Forwarding.


Users may direct questions to sys-help@loni.org.

Powered by MediaWiki