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

VMD includes a Virtual DNA Viewer plugin which can be used to render images of chromatin using ideal DNA interbasepair helical parameters (in proper r.h.s. ref. frame ordering). This plugin is useful for investigating the folding of chromatin based on the "two-angle" model where the total linker length and twist between nucleosomes determines the overall geometry of chromatin. This is an example of the type of visualizations that can be done with VMD using mathematical models and equations rather than all-atom structure data.
Other Spotlights

Overview

Molecular representations
Molecular file formats
GPU-accelerated computing
Interactive molecular dynamics
Programs that use VMD
VMD research publications
How to cite VMD
VMD citation list, (12,743 as of May'14)

Download

Download (all versions)
VMD 1.9.2 (MacOS X, Unix, Windows)
VMD 1.9.1 (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

Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail, Winner SC'14 Visualization and Data Analytics Showcase
Petascale Tcl with NAMD, VMD, and Swift/T
VMD 1.9.2 beta 1 posted for download
Optimizing VMD on GPU-accelerated ARM platforms
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.
Past announcements

Gallery

Gallery of Posters, Images, and Movies made with VMD
VMD running in the NanoDome at Temple University

Development

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