J Comput Chem. 2009 Apr 30;30(6):864-72.

Accelerating molecular dynamic simulation on graphics processing units.

Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS.

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Department of Bioengineering, Stanford University, Stanford, California 94305, USA.

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.

PMID:: 19191337; [PubMed - indexed for MEDLINE]
PMCID: PMC2724265

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