vmd

Summary

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

License:. Using VMD requires to agree and conform with the license! Any commercial use of VMD requires a commercial license!

Path: /software/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 initialize the environment with the module command:

[elx]% module load maxwell
[elx]% module avail vmd
[elx]% module load vmd  # also part of gromacs modules.