Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems

Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.

Original languageEnglish
Pages (from-to)110-118
Number of pages9
JournalJournal of Computational Chemistry
Volume30
Issue number1
DOIs
Publication statusPublished - 2009 Jan 15

Keywords

  • Cutoff method
  • Ewald method
  • High-performance computing
  • MDGRAPE-3
  • Special-purpose computer

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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