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VMD (Visual Molecular Dynamics) is an open source molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

  • 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, and others.
  • VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.
  • 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.

VMD User's Guide

VMD Tutorial


VMD is available from MobileVisLab.

To run the software, type vmd at the prompt.


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