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GROMACS
GROMACS is a molecular dynamics package designed primarily for simulation of biochemical molecules like proteins, lipids, and nucleic acids that have a lot complicated bonded interactions. The CUDA port of GROMACS enabling GPU acceleration is now available in beta and supports Particle-Mesh-Ewald (PME), arbitrary forms of non-bonded interactions, and implicit solvent Generalized Born methods.
Download and Installation
Benchmark Data
The CUDA version of GROMACS currently supports a single GPU and produces the following results:
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| Data courtesy of Stockholm Center for Biomembrane Research |
Technical Papers
- M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., 30(6):864-872. (2009)
- More publications on accelerating molecular dynamics applications using GPUs
- More publications on accelerating quantum chemistry applications using GPUs
Discussion Forums
GPU SOLUTIONS
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 |
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WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk
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DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations
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