LC Hotline: 2-4531

From offsite: (925) 422-4531

 

Hours

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

 

VMD

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.

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.

Environment

Machines and Versions

See LC graphics software page.

Location

/usr/global/tools/vmd

Settings

It is recommended that you use dotkit to set up your environment. 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.

Usage

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 put 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.

Help

Help is available on the VMD home page. There you will find VMD community pages, tutorials, manuals, a 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@llnl.gov, (925) 422-4531.

Download

You can install VMD on your local workstation. See the Download section of the VMD Home Page for information on downloading VMD.

Links

 

UCRL-MI-128467-REV-1