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

• Published in: Computer journal Vol. 54; no. 7; pp. 1181 - 1187
• Main Authors: Narumi, Tetsu, Yasuoka, Kenji, Taiji, Makoto, Zerbetto, Francesco, Höfinger, Siegfried
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01-07-2011; Oxford Publishing Limited (England)
• Subjects: Accelerators; Algorithms; Biology; Computational efficiency; Computer science; Electrostatics; Hardware; Integrated circuits; Mathematical analysis; Molecular biology; Web services; ASIC; ESP; implicit solvation models; Poisson Boltzmann; MDGRAPE-3; GPU
• ISSN: 0010-4620; 1460-2067
• DOI: 10.1093/comjnl/bxq079

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 27×. Once ESP computations have become a matter of seconds, the underlying application can be offered in the form of a web service.