CSB Home | Search | Table of Contents | General Information

VMD v1.7.1

VMD is a molecular visualization and analysis program designed to be easy to use and modify. It was created by the Theoretical Biophysics Group at the University of Illinois and the Beckman Institute.

To run VMD from an SGI, Linux or a Dec Alpha in the CSB core, type:


VMD has also been installed on the Windows machines in the Core.

The online Users Guide, is also available as a pdf document.
A hard copy of the Users Guide is in the core area.

Note: See local details for output as POV-Ray command file.

Note: The HELP button on the Main Menu does not work. Use the link here.


Input Formats

VMD reads X-PLOR style PSF, PDB, and DCD files. In addition, if Babel is installed, the following formats can be automatically converted into PDB files and read into VMD:

Alchemy,                  AMBER PREP,               Ball and Stick,           
Biosym .CAR,              Boogie,                   Cacao Cartesian,          
Cambridge CADPAC,         CHARMm,                   Chem3D Cartesian 1,       
Chem3D Cartesian 2,       CSD CSSR,                 CSD FDAT,                
CSD GSTAT,                Free Form Fractional,     GAMESS Output,           
Gaussian Z-Matrix,        Gaussian Output,          Hyperchem HIN,           
Mac Molecule,             Macromodel,               Micro World,              
MM2 Input,                MM2 Ouput,                MM3,                     
MMADS,                    MDL MOLfile,              MOLIN,                   
Mopac Cartesian,          Mopac Internal,           Mopac Output,             
                          ShelX,                    Sybyl Mol,               
Sybyl Mol2,               and XYZ.                  

Molecular Representations

Molecules may be drawn as lines, bonds, CPK, licorice, VDW spheres, ribbons, tubes, surface, secondary structure cartoons, etc. and colored by atom, residue, segment, or molecule as well as by mass, charge, occupancy, position, etc. By using VMD's powerful atom selection language, multiple molecular representations may be applied to arbitrary groups of atoms simultaneously.

3D Display

VMD's display objects are nearly device independent, allowing the system to be used with a regular screen, stereo shutter glasses, head-mounted displays, and the CAVE. VMD also supports several 3D tracking devices through the UNC tracker library.

Photorealistic Output

Additional display objects allow VMD to write input files for the popular rendering packages

POV-Ray and

to produce photorealistic images suitable for film recorders, etc. VMD can also read and display Raster3D input scripts.

Simulation Display and Control

VMD can play DCD trajectory files to show results of MD simulations. VMD allows interactive display and control of running simulations when used with the parallel molecular dynamics code namd.

Scripting Language

All of VMD's functions can be accessed through text commands implemented in Tcl. This allows scripts to be written which can load molecules or run entire demos automatically. These scripts can include control loops, variable substitution, if-then-else constructs, function and procedure definitions, and many other features.

Many script extensions have been added to Tcl for analyzing molecular structures. These include methods for extracting atomic and molecular information, vector and matrix routines for some numerical work, and 3D graphics commands for displaying the results.

We maintain a library of interesting and useful scripts.

The authors request that any published work which utilizes VMD please include the following reference:
Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38

CSB Home | Search | Table of Contents | General Information

Center for Structural Biology (www.csb.yale.edu), Yale University (www.yale.edu)
Contact: webadmin(at)mail^csb^yale^edu
Last Modified: Tuesday, 29-Jan-2002 10:07:50 EST by Shanti Kunchaparty