VMD

The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.0 of the program VMD, a new package for the graphical display and visualization of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and a precompiled binary for Silicon Graphics workstations running version 5 or later of the IRIX operating system. The documentation, in postscript form, includes an installation guide, a users guide, and a programmers guide for interested researchers. VMD also provides on-line help through the use of an external HTML viewer such as Mosaic or Netscape.

Obtaining VMD: A more complete description of VMD is available via the VMD WWW home page which is located at http://www.ks.uiuc.edu/Research/vmd/

The software itself is available via anonymous ftp in the directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/ (please see the README file in this directory for the latest version info).

Features: VMD is designed for the visualization 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, 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.

The program has many features, which include:

  • 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 write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, and Raster3D.

  • Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities.

  • Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code structure;

  • 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 info: http://www.ks.uiuc.edu:1250/Research/namd

VMD can be used to set up and concurrently display a MD simulation using namd. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment.

Availability: VMD runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library (a commercial port of the SGI GLlibrary, available from Portable Graphics, Inc.) is available on your system. Two versions of the distribution are available, one including the complete VMD source code, and one which just includes a precompiled VMD executable for SGI IRIX version 5.

VMD, namd, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. This project is funded by the National Institutes of Health and the National Science Foundation.



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