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Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

Gines D. Guerrero, Horacio Perez-Sanchez, Wolfgang Wenzel, Jose M. Cecilia, Jose M. Garcia
Grupo de Arquitectura y Computacion Paralela, Dpto. de Ing. y Tecnologia de Computadores, Facultad de Informatica, Universidad de Murcia, Campus de Espinardo 30100, Murcia, Spain
5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), 2011

@inproceedings{guerrero2011effective,

   title={Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs},

   author={Guerrero, G. and P{‘e}rez-S{‘a}nchez, H. and Wenzel, W. and Cecilia, J. and Garc{‘i}a, J.},

   booktitle={5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)},

   pages={63–69},

   year={2011},

   organization={Springer}

}

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In this work we discuss the benefits of using massively parallel architectures for the optimization of Virtual Screening methods. We empirically demonstrate that GPUs are well suited architecture for the acceleration of non-bonded interaction kernels, obtaining up to a 260 times sustained speedup compared to its sequential counterpart version.
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