vmd Overview

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.


To load the VMD executable into the environment, run:
$ module load vmd
$ vmd
This will launch VMD (make sure X11 forwarding is enabled to be able to use the graphical interface). At the VMD prompt, type
vmd> draw cylinder {0 0 0} {4 0 0} radius 0.1
This will draw a cylinder on the screen. More cylinders or other shapes/text/lines can be added to the image.
vmd> draw cone {4 0 0} {5 0 0} radius 0.15
vmd> draw text {5 0 0} "This way"
Replacing "cylinder" with "sphere" or "line", etc will draw the respective shape. For more in depth tutorials and information see the VMD User's Guide: http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html


  • vmd@1.9.3%gcc@4.4.7
  • vmd@1.9.3%gcc@4.4.7