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Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst
School of Chemistry, University of Nottingham, University Park, Nottingham, NG7?2RD
Molecular Informatics, Volume 30, Issue 6-7. (2011), pp. 498-504

@article{bakermolecular,

   title={Molecular Dynamics Simulations Using Graphics Processing Units},

   author={Baker, J.A. and Hirst, J.D.},

   journal={Molecular Informatics},

   publisher={Wiley Online Library},

   year={2011}

}

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It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.
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