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VMD

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General Description

VMD stands for Visual Molecular Dynamics. It is used for molecular modeling and visualization for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

VMD is primarily developed as a tool for viewing and analyzing the results of molecular dynamics simulations, but it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects.

Basic Usage

 module load vmd

 vmd

Then in vmd interface,

 vmd > help
 vmd > exit

Useful Options

The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum:

Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. 

Further Information

See the official website: VMD