2943

Accelerating Energy Minimization using Graphics Processors

Bharat Sukhwani, Martin C. Herbordt
Department of Electrical and Computer Engineering, Boston University
Symposium on Application Accelerators in High Performance Computing, 2009 (SAAHPC’09)

@article{sukhwani2009accelerating,

   title={Accelerating Energy Minimization using Graphics Processors},

   author={Sukhwani, B. and Herbordt, M.C.},

   booktitle={Symposium on Application Accelerators in High Performance Computing, SAAHPC},

   year={2009}

}

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Energy minimization is an important step in molecular modeling, with applications in molecular docking and in mapping binding sites. Minimization involves repeated evaluation of various bonded and non-bonded energies of a protein complex. It is a computationally expensive process, with runtimes typically being many hours on a desktop system. In the current article, we present the acceleration of the energy evaluation phase of minimization on a graphics processor, resulting in an 11x total speedup compared with a single core of a desktop machine.
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