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.
Human immunodeficiency virus type 1 (HIV-1) is the major cause of
AIDS, for which treatments need to be developed continuously as the
virus becomes quickly resistant to new drugs. When the virus infects
a human cell it releases into the cell its capsid, a closed, stable
container protecting the viral genetic material. However, interaction
with the cell triggers at some point an instability of the capsid,
leading to a well timed release of the genetic material that merges
then with the cell's genes and begins to control the cell. The dual
role of the capsid, to be functionally both stable and unstable, makes
it in principle an ideal target for antiviral drugs and, in fact,
treatments of other viral infections successfully target the
respective capsids. The size of the HIV-1 capsid (about 1,300
proteins), and its irregular shape had prevented so far the resolution
of a full capsid atomic-level structure. However, in a tour de force
effort, groups of experimental and computational scientists have now
resolved the capsid's chemical structure (deposited to the protein
data bank under the accession codes 3J3Q
recently (see also journal cover), the
researchers combined NMR structure analysis, electron microscopy and
data-guided molecular dynamics
simulations utilizing VMD to prepare
and analyze simulations performed using NAMD on one of the most powerful computers
Waters, to obtain and characterize the HIV-1 capsid. The
discovery can guide now the design of novel drugs for enhanced
More information is available on our virus website, in video, and in a press release.
See also movie: 15.5MB
made with VMD
News and Announcements
GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting, FD169, 2014.
Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems, FD169, 2014.
Webinar: GPU-Supercharged Molecular Visualization / Analysis with VMD
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