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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

The Tesla Bio Workbench applications can be deployed on GPU-based desktop personal supercomputers or in data center solutions. Built on the revolutionary massively parallel CUDA architecture, these solutions are designed to accelerate the pace of computational science.

RECOMMENDED HARDWARE CONFIGURATION

Desktop Workstation Configuration	Data Center Configuration
GPUs 4 Tesla C1060 Computing GPUs + onboard GPU for visualization OR 3 Tesla C1060 GPUs + 1 Quadro FX5800 GPU for visualization CPU and Main Memory 2.33 GHz x86 CPU 4 GB main memory per Tesla C1060 GPU	Not applicable (VMD is a desktop visualization application)

WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk Learn more > Where to buy >		DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations Learn more > Where to buy >