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A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Nathan Schmid, Mathias Botschi, Wilfred F. Van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zurich 8093, Switzerland
Journal of Computational Chemistry, Volume 31, Issue 8, pages 1636-1643, June 2010

@article{schmid2010gpu,

   title={A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software},

   author={Schmid, N. and B{\”o}tschi, M. and Van Gunsteren, W.F.},

   journal={Journal of Computational Chemistry},

   volume={31},

   number={8},

   pages={1636–1643},

   issn={1096-987X},

   year={2010},

   publisher={Wiley Online Library}

}

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During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent-solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed-ups up to a factor of 54 (single-precision GPU vs. double-precision CPU) could be achieved. The accuracy of the single-precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent-solvent interaction evaluation on a GPU, and thus, to speed-up their simulations by a factor 6-9.
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