VMD is a molecular visualization program for displaying, animating,
and analyzing large biomolecular systems using 3-D graphics and
VMD supports computers running MacOS X, Unix, or Windows,
is distributed free of charge, and includes source code.
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.
News and Announcements
2014 VMD Calendar
GPU-accelerated molecular visualization on petascale supercomputing platforms, UltraVis'13
Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters, Proc. XSCALE, 2013.
Rapid parameterization of small molecules using ffTK, JCC, 2013.
Most cited since 2008: "GPU-Accelerated Molecular Modeling Coming of Age"
VMD QuickSurf rendering of HIV-1 capsid on cover of Nature 497 (7451), 2013.
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation, J. Comp. Chem, 2013.
Force Field Toolkit (FFTK) tutorial screencasts
Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories, EuroVis 2012.
Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories, LNCS, 2011.
Gallery of Posters, Images, and Movies made with VMD
VMD running in the NanoDome at Temple University
VMD User Survey Results
VMD development status and pre-release test downloads
CVS source code access
VMD Programmer's documentation