VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Several key kernels and applications in VMD now take advantage of the massively parallel CUDA architecture of NVIDIA’s GPUs. These applications run 20x to 100x faster when using a NVIDIA CUDA GPU compared to running them on a CPU only and are discussed below.

Download and Installation

• Download VMD 1.8.7 Binaries (from UIUC)
• Release Notes

Benchmark Data

Data courtesy of Theoretical and Computational Bio-physics Group, UIUC

There are several detailed benchmarks on VMD using GPUs at NVIDIA’s VMD benchmark page.

Presentations

• Publications and presentations on GPU acceleration in VMD and NAMD by Klaus Schluten’s Group
• From SC09: Accelerating Molecular Modeling Applications with GPU Computing - John Stone, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign
• From 2009 GPU Technology Conference: GPU Accelerated Visualization and Analysis in VMD - John Stone, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign
• More publications on accelerating molecular dynamics applications using GPUs

Interviews / Videos

• From SC09: John Stone of University of Illinois Talks About Running VMD 412x Faster with GPUs
• SC09 BLOG on NVIDIA nTersect: Studying the H1N1 Virus using NVIDIA GPUs

Discussion Forums

• GPU computing communities on GPUcomputing.net

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