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 provides user-editable "materials" which can be applied to molecular geometry. These material properties control the details of how VMD shades the molecular geometry, and how transparent or opaque the displayed molecular geometry is. With this feature, one can easily create nice looking transparent surfaces which allow inner structural details to be seen within a large molecular structure. The material controls can be particularly helpful when rendering molecular scenes using external ray tracers, each of which typically differ slightly.
Other Spotlights

Overview

Molecular representations
VMD plugin library
Molecular file formats
GPU-accelerated computing
Interactive molecular dynamics
Programs that use VMD
VMD research publications
How to cite VMD
VMD citation list (17,617 as of Mar'16)

Download

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

Molecular dynamics-based model refinement and validation for sub-5Å cryo-electron microscopy maps, eLife 2016
Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering, HPDAV 2016
High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL, HPDAV 2016
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads, HCW 2016
Example VMD VR/3-D YouTube videos
Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing, J. Par. Comp. 2016
Chemical Visualization of Human Pathogens: the Retroviral Capsids, SC'15 Viz. Showcase (YouTube)
VMD 1.9.2 image making tutorial video (YouTube)
Multilevel Summation Method for Electrostatic Force Evaluation, JCTC 2015
Updated Gromacs plugins for VMD 1.9.2
VMD 1.9.2 Released
Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail, SC'14
Petascale Tcl with NAMD, VMD, and Swift/T, HPTCDL'14
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.
Past announcements

Gallery

Winning SC'14 chromatophore light harvesting visualization
VMD movie gallery on YouTube
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