VMD

From ScientificComputing
Revision as of 10:34, 12 December 2016 by Sfux (talk | contribs) (Created page with "{{Application}}")

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Category

Visualization, Chemistry

Description

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.

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions
1.9.2

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
1.9.2 module load gcc/4.8.2 vmd/1.9.2 legacy centos_cruft/6

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Interactive session

In order to start an interactive VMD session on a login node, you need to login with X11 forwarding enabled. After loading the required modules
module load gcc/4.8.2 vmd/1.9.2
you can start the interactive session with the command VMD.

License information

VMD license

Links

http://www.ks.uiuc.edu/Research/vmd

https://en.wikipedia.org/wiki/Visual_Molecular_Dynamics