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Molecular Dynamics Simulations on Commodity GPUs with CUDA

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Muller-Wittig
School of Computer Engineering, Nanyang Technological University, Centre for Advanced Media Technology
High Performance Computing – HiPC 2007 In High Performance Computing – HiPC 2007, Vol. 4873 (2007), pp. 185-196.

@conference{liu2007molecular,

   title={Molecular dynamics simulations on commodity GPUs with CUDA},

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

   booktitle={Proceedings of the 14th international conference on High performance computing},

   pages={185–196},

   isbn={3540772197},

   year={2007},

   organization={Springer-Verlag}

}

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Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) to design and implement a new parallel algorithm. This results in an implementation with significant runtime savings on an off-the-shelf computer graphics card.
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