Summary
Source: http://www.ks.uiuc.edu/Research/vmd/
License: Please see http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html. Using VMD requires to agree and conform with the license! Any commercial use of VMD requires a commercial license!
Path: /opt/vmd
Documentation: http://www.ks.uiuc.edu/Research/vmd/current/docs.html
Citation: The user agrees that any reports or published results obtained with the Software will acknowledge its use by the appropriate citation as follows: "VMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign." Any published work which utilizes VMD shall include the following reference: "Humphrey, W., Dalke, A. and Schulten, K., `VMD -Visual Molecular Dynamics', J. Molecular Graphics, 1996, vol. 14, pp. 33-38.". Electronic documents will include a direct link to the official VMD page at http://www.ks.uiuc.edu/Research/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.
Using VMD
VMD doesn't require a special setup. To add it to your PATH either add /opt/vmd/bin to $PATH or initialize the environment use the module command:
[elx]% module avail [elx]% module load md # initialized vmd and a few other tools [elx]% which vmd /opt/vmd/bin/vmd [elx]% vmd