Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger
Faculty of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, 182-8585 Chofu-shi, Tokyo, Japan
The Computer Journal


   title={Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3},

   author={Narumi, T. and Yasuoka, K. and Taiji, M. and Zerbetto, F. and H{\”o}finger, S.},

   journal={The Computer Journal},



   publisher={Br Computer Soc}


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Electrostatic potentials (ESPs) are frequently used in structural biology for the characterization of biomolecules. Here we study the potential employment of hardware accelerators like the graphics processing unit or the application-specific integrated circuit MD-GRAPE-3 for the purpose of efficient computation of ESPs. An algorithm closely coupled to the general description of molecular surfaces is ported to both specialized architectures. The high-level interface library MR1/3 is used, which greatly simplifies the porting process. Hardware-accelerated versions show significant Speed-Up factors reaching values of up to 27x. Once ESP computations have become a matter of seconds, the underlying application can be offered in the form of a web service.
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