Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi; Kenji Yasuoka; Makoto Taiji; Francesco Zerbetto; Siegfried Höfinger

doi:10.1093/comjnl/bxq079

Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Höfinger

Department of Mechanical Engineering

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1181-1187
Number of pages	7
Journal	Computer Journal
Volume	54
Issue number	7
DOIs	https://doi.org/10.1093/comjnl/bxq079
Publication status	Published - 2011 Jul 1

Keywords

ASIC
ESP
GPU
MDGRAPE-3
Poisson Boltzmann
implicit solvation models

ASJC Scopus subject areas

Computer Science(all)

Access to Document

10.1093/comjnl/bxq079

Cite this

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abstract = "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.",

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AU - Yasuoka, Kenji

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AU - Zerbetto, Francesco

AU - Höfinger, Siegfried

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AB - 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.

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Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3

Abstract

Keywords

ASJC Scopus subject areas

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