VMD - Visual Molecular Dynamics

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
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Spotlight

Because oxygen gas is very reactive, it is frequently employed by the cell as a reagent by proteins called enzymes, which build the organic compounds that the cell needs. One such enzyme belongs to the copper amine oxidase family. These proteins transform amine-containing compounds into molecules needed by the cell, by reacting the compounds with oxygen. Researchers have long been interested in finding out how the various reagents reach the buried copper active site before the final oxidation reaction can occur. While copper amine oxidases exhibit an obvious channel for capturing the amine compounds to be modified, it had been unclear until now how oxygen molecules make their way through the enzyme. With the help of computer simulations using NAMD, researchers have identified in a recent publication, the routes taken by oxygen inside various copper amine oxidases from different species. In order to accomplish this, they analyzed simulations of the motions of four copper amine oxidases, using the VMD analysis and visualization software, which can predict the probability of finding oxygen molecules anywhere inside the simulated proteins. This analysis found numerous oxygen conduction routes inside each copper amine oxidase, i.e., oxygen can enter the protein through many routes, as it would in a sponge. More information on finding O2 migration pathways in proteins can be found here.
Other Spotlights
Copper amine oxidase

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Overview

Molecular representations
Supported molecular file formats
GPU-accelerated computing
Interactive molecular dynamics
Required software
Programs that use VMD
VMD publications
How to cite VMD, Papers citing VMD

Download

Download (all versions)
VMD 1.8.6 (MacOS-X, Unix, Windows)
VMD plugin library
VMD script library
License, Copyright and Disclaimer

Documentation and Support

User and installation guides
Quick help
FAQ
VMD-L mailing list
Bug List

News and Announcements

2009 VMD Calendar
VMD/NAMD at SC2008 conference, Nov 15-21, 2008
NVIDIA Appoints First CUDA Center of Excellence
Using VMD - an introductory tutorial Current Protocols - Bioinformatics, 2009. In press.
Membrane Structural Biology book cover made with VMD
GPU accelerated cutoff pair potentials paper, ACM Computing Frontiers, pp. 273-282, 2008
GPU Computing paper, Proceedings of the IEEE, 96:879-899, 2008
J. Comp. Chemistry cover image made with VMD
GPU-accelerated molecular modeling paper, J. Comp. Chem, 28:2618-2640, 2007
Nature Biotechnology cover image made with VMD (Jul 2007)
VMD 1.8.6 (MacOS-X, Unix, Windows) (Apr 2007)
VMD outline rendering style inspired by the work of David S. Goodsell (Apr 2007)
Create 3-D PDFs with VMD and Acrobat3D (Feb 2007)
Advanced VMD/Tachyon figure rendering (Feb 2007)
VMD Images and Movies Tutorial (Jan 2007)
Past announcements

Gallery

Gallery of Posters, Images, and Movies made with VMD
Events and tutorial picture gallery

Development

VMD User Survey Results
VMD development status and pre-release test downloads
CVS source code access
VMD Programmer's documentation

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