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Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Ji Xu, Ying Ren, Wei Ge, Xiang Yu, Xiaozhen Yang, Jinghai Li
State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering (IPE), Chinese Academy of Sciences, P.O. Box 353, Beijing 100190
arXiv:1001.3764v1 [physics.comp-ph] (21 Jan 2010)

@article{xu2010molecular,

   title={Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit},

   author={Xu, J. and Ren, Y. and Ge, W. and Yu, X. and Yang, X. and Li, J.},

   journal={Arxiv preprint arXiv:1001.3764},

   year={2010}

}

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Molecular dynamics (MD) simulation is a powerful computational tool to studythe behavior of macromolecular systems. But many simulations of this field arelimited in spatial or temporal scale by the available computational resource.In recent years, graphics processing unit (GPU) provides unprecedentedcomputational power for scientific applications. Many MD algorithms suit withthe multithread nature of GPU. In this paper, MD algorithms for macromolecularsystems that run entirely on GPU are presented. Compared to the MD simulationwith free software GROMACS on a single CPU core, our codes achieve about 10times speed-up on a single GPU. For validation, we have performed MDsimulations of polymer crystallization on GPU, and the results observedperfectly agree with computations on CPU. Therefore, our single GPU codes havealready provided an inexpensive alternative for macromolecular simulations ontraditional CPU clusters and they can also be used as a basis to developparallel GPU programs to further speedup the computations.
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