LC Hotline: 2-4531

From offsite: (925) 422-4531

 

Hours

Monday–Friday
8am–12pm, 1–4:45pm
B453 R1103 | Q-clearance area

 

VMD

Last Verified : 2018-12-19

Overview

VMD (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 computer.

VMD is developed by the Theoretical and Computational Biophysics Group (TCBG) of the University of Illinois at Urbana-Champaign.

Environment

Machines and Versions

See LC visualization software page.

Location

Links to the latest version exist in /usr/tce/bin

Multiple versions may be accessible via modules. Type module avail vmd to see the available options. You can specify a particular version in the module command, e.g. module load vmd/1.9.3

The actual installation directories are in /usr/tce/packages/vmd

Settings

The module load vmd command will setup your PATH and any other needed environment variables.

To enable stereo, start VMD by typing vmd_stereo. Stereo is disabled by default because it conflicts with certain implementations of X11.

Usage

As a convenience, you can just type vmd to start the latest version of VMD from /usr/tce/bin. If this does not work, try typing module load vmd before running vmd.

If you use VMD, you must abide by the license agreement.

Help

Help is available on the VMD home page. There you will find VMD community pages, tutorials, manuals, an 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.

Help is available from the LC Hotline: lc-hotline@llnl.gov, (925) 422-4531

Download

You can install VMD on your local workstation. See the VMD website's Download page for information on downloading VMD.

Links

UCRL-MI-128467-REV-1