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Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande
Department of Bioengineering, Stanford University, Stanford, California 94305
Journal of Computational Chemistry, Vol. 30, No. 6. (30 April 2009), pp. 864-872.

@article{friedrichs2009accelerating,

   title={Accelerating molecular dynamic simulation on graphics processing units},

   author={Friedrichs, M.S. and Eastman, P. and Vaidyanathan, V. and Houston, M. and Legrand, S. and Beberg, A.L. and Ensign, D.L. and Bruns, C.M. and Pande, V.S.},

   journal={Journal of computational chemistry},

   volume={30},

   number={6},

   pages={864–872},

   issn={1096-987X},

   year={2009},

   publisher={Wiley Online Library}

}

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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
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