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General purpose molecular dynamics simulations fully implemented on graphics processing units

J. Anderson, C. Lorenz, A. Travesset
Ames Laboratory and Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
Journal of Computational Physics, Vol. 227, No. 10. (01 May 2008), pp. 5342-5359.

@article{anderson2008general,

   title={General purpose molecular dynamics simulations fully implemented on graphics processing units},

   author={Anderson, J.A. and Lorenz, C.D. and Travesset, A.},

   journal={Journal of Computational Physics},

   volume={227},

   number={10},

   pages={5342–5359},

   issn={0021-9991},

   year={2008},

   publisher={Elsevier}

}

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Graphics processing units (GPUs), originally developed for rendering real-time effects in computer games, now provide unprecedented computational power for scientific applications. In this paper, we develop a general purpose molecular dynamics code that runs entirely on a single GPU. It is shown that our GPU implementation provides a performance equivalent to that of fast 30 processor core distributed memory cluster. Our results show that GPUs already provide an inexpensive alternative to such clusters and discuss implications for the future.
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