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

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

Research output: Contribution to journalArticle

10 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 languageEnglish
Pages (from-to)1181-1187
Number of pages7
JournalComputer Journal
Volume54
Issue number7
DOIs
Publication statusPublished - 2011 Jul

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Application specific integrated circuits
Electrostatics
Hardware
Biomolecules
Web services
Particle accelerators
Graphics processing unit

Keywords

  • ASIC
  • ESP
  • GPU
  • implicit solvation models
  • MDGRAPE-3
  • Poisson Boltzmann

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3. / Narumi, Tetsu; Yasuoka, Kenji; Taiji, Makoto; Zerbetto, Francesco; Höfinger, Siegfried.

In: Computer Journal, Vol. 54, No. 7, 07.2011, p. 1181-1187.

Research output: Contribution to journalArticle

Narumi, Tetsu ; Yasuoka, Kenji ; Taiji, Makoto ; Zerbetto, Francesco ; Höfinger, Siegfried. / Fast calculation of electrostatic potentials on the GPU or the ASIC MD-GRAPE-3. In: Computer Journal. 2011 ; Vol. 54, No. 7. pp. 1181-1187.
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