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GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu
Molecular Dynamics Group, University of Groningen, Groningen, The Netherlands
IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), 2012

@inproceedings{goga2012gpu,

   title={GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations},

   author={Goga, Nicolae and Marrink, Siewert and Cioromela, Ruxandra and Moldoveanu, Florica},

   booktitle={Bioinformatics & Bioengineering (BIBE), 2012 IEEE 12th International Conference on},

   pages={251–254},

   year={2012},

   organization={IEEE}

}

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This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands. One should note that molecular dynamics simulations are time-consuming simulations of systems, running time ranging from days to weeks and months. Therefore parallelization is a key issue for the well-running and use of MD software. The paper presents the main ingredients of GPU parallelization of the new algorithms and simulation results. It can be concluded that the parallelization through the use of graphical cards improves the performances of the runs as compared to the serial version of the code.
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