VMD at NERSC
Table of Contents
- VMD is a molecular visualization program for displaying, animating,
and analyzing large biomolecular systems using 3-D graphics and scripting.
The current default version of VMD is 1.8.
VMD has a rich set of functionality for performing Visual Molecular Dynamics.
A complete list of the functionality, Image Gallery, technical tips, etc.,
can be found at
the main VMD web site.
- Accessing VMD
VMD is available on NERSC platforms
via the modules facility.
Links to online local documentation (pdf/html format).
- Additional Resources
Links to the VMD distribution site, supplemental information, a FAQ
- Sample Screen Shots.
- 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, 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
- VMD supports computers running MacOS-X, Unix, or Windows, is
distributed free of charge, and includes source code.
- No limits on the number of molecules, atoms, residues or
number of animation frames, except available memory.
- Many molecular rendering and coloring methods.
- Stereo display capability.
- Extensive atom selection syntax for choosing subsets of atoms for
display (includes boolean operators, regular expressions, and more).
- Integration with the program 'Babel' which allows VMD to read many
molecular data file formats. Even without the use of Babel,
VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
binary DCD files and X-PLOR compatible PSF files.
- Ability to export displayed graphics to files which may be
processed by a number of popular ray tracing and image rendering
packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
- Extensive graphical and text-based user interfaces, which use the
Tcl package to provide full scripting capabilities.
- Extensions to the Tcl language which enable researchers to write
their own routines for molecular analysis.
- Modular, extensible source code using an object-oriented design in
C++, with a programmers guide describing the source code.
- Integration with the program NAMD, a fast, parallel, and scalable
molecular dynamics program developed in conjunction with VMD
in the Theoretical Biophysics Group at the University of Illinois.
See the NAMD WWW home page for more information:
- VMD works well with projected display systems like the
3-D Projection Facility maintained by the Theoretical Biophysics
- VMD can be used to concurrently display and interact with a
running MD simulation using NAMD.
To access vmd on NERSC platforms, use the modules facility as follows:
% module load vmd
Local Documentation Downloads: (Use shift left-mouse to download files)
Sample Screen Shots