(Visual Molecular Dynamics)
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, 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
Starting with version 1.8.7, VMD is able to use CUDA on edge.llnl.gov
for a speedup in rendering complex models.
VMD is developed by the Theoretical and Computational Biophysics Group
(TCBG) of the University of Illinois at Urbana-Champaign.
Settings: It is recommended that you use dotkit
to set up your envirnoment. Typing use
vmd will enable the latest version of VMD. To use another
version, for example 1.8.6, use vmd186
. To enable stereo, type use
vmd-stereo . Stereo is disabled by default in version 1.8.7
because it conflicts with certain Macintosh implementations of X11. For
convenience, running /usr/local/bin/vmd will set up your environment and run the latest version of vmd.
To start up VMD, just type vmd . See the Settings section above for other dotkit variants you can use. If you use VMD frequently, you
might find it convenient to pu t use -q
vmd (or whatever version you prefer) in your startup file (.cshrc or .bashrc for example). Be
sure to use the -q option.
If you use VMD, you must abide by the license agreement
There is a lot of help available on the VMD Home
. There you will find VMD Community Pages, tutorials, manuals,
faq, access to a VMD mailing list and more. You can also view sample
images and movies to get a better idea of the capabilities of VMD.
You can install VMD on your local workstation. See the Download section
of the VMD Home Page
for information on downloading VMD.