Visual Molecular Dynamics (VMD)

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

It can be used to view more general molecules, as VMD reads standard Protein Data Bank (PDB) files and display the contained structure.  VMD provides a wide variety of methods for rendering and coloring molecule.  VMD can be used to animate and analyze the trajectory of molecular dynamics (MD) simulations, and can interactively manipulate molecules being simulated on remote computers (Interactive MD).

VMD 1.8.6

Price Free to download Size 17.2MB License Freeware Developer University of Illinois at Urbana-Champaign Website ks.uiuc.edu/Research/vmd System Requirements GL or OpenGL based 3-D rendering libraries Other programs required to use optional features Support Sites: Documentation Selected Reviews:

Features include:

• Support for GPU accelerated computation
  
• No limits on the number of molecules, atoms, residues or number of trajectory frames, except available memory
• Fendering mode which supports scene capture with Adobe Acrobat3D, allowing researchers to create PDF documents containing 3-D scenes from VMD
• Many molecular rendering and coloring methods including support for high-quality molecular scene rendering using Tachyon, NVIDIA Gelato, and PIXAR RenderMan
• Stereo display capability
  
• Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more)
  
• Support for over 60 molecular file formats and data types through an extensive library of built-in file reader/writer plugins and translators VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids.
  
• 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 Tachyon.
  
• User-extensible graphical and text-based user interfaces, built-on standard Tcl/Tk and Python scripting languages
  
• 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 program architecture and source code
• Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program
• VMD tutorials developed locally, and by the research community at large

Last Updated Saturday, September 20 2008 @ 07:19 AM EDT