1096-987X/asset/olbannerleft.gif?v=1&s=6a06c9acc9d19b9514883204cd54b2fb803be905)
1096-987X/asset/olbannerright.gif?v=1&s=5c13c2b5f418bc7a48bf448d9b71c474e504844e)
Accelerating molecular dynamic simulation on graphics processing units
Article first published online: 3 FEB 2009
DOI: 10.1002/jcc.21209
Copyright © 2009 Wiley Periodicals, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
Additional Information
How to Cite
Friedrichs, M. S., Eastman, P., Vaidyanathan, V., Houston, M., Legrand, S., Beberg, A. L., Ensign, D. L., Bruns, C. M. and Pande, V. S. (2009), Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem., 30: 864–872. doi: 10.1002/jcc.21209
Publication History
- Issue published online: 11 MAR 2009
- Article first published online: 3 FEB 2009
- Manuscript Accepted: 13 DEC 2008
- Manuscript Revised: 12 DEC 2008
- Manuscript Received: 19 SEP 2008
Funded by
- Simbios via the NIH Roadmap for Medical Research. Grant Numbers: U54 GM072970, NIH R01-GM062868, NSF EF-0623664
- Abstract
- Article
- References
- Cited By
Keywords:
- GPU;
- molecular dynamics;
- implicit solvent
Abstract
We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009