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Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

W. Liu, B. Schmidt, G. Voss, W. Mullerwittig
School of Computer Engineering, Nanyang Technological University, Singapore 639798
Computer Physics Communications, Vol. 179, No. 9. (01 November 2008), pp. 634-641

@article{liu2008accelerating,

   title={Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA},

   author={Liu, W. and Schmidt, B. and Voss, G. and M{\”u}ller-Wittig, W.},

   journal={Computer physics communications},

   volume={179},

   number={9},

   pages={634–641},

   issn={0010-4655},

   year={2008},

   publisher={Elsevier}

}

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Molecular dynamics is an important computational tool to simulate and understand biochemical processes at the atomic level. However, accurate simulation of processes such as protein folding requires a large number of both atoms and time steps. This in turn leads to huge runtime requirements. Hence, finding fast solutions is of highest importance to research. In this paper we present a new approach to accelerate molecular dynamics simulations with inexpensive commodity graphics hardware. To derive an efficient mapping onto this type of computer architecture, we have used the new Compute Unified Device Architecture programming interface to implement a new parallel algorithm. Our experimental results show that the graphics card based approach allows speedups of up to factor nineteen compared to the corresponding sequential implementation.
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