Hardware accelerator for molecular dynamics: MDGRAPE-2

Ryutaro Susukita, Toshikazu Ebisuzaki, Bruce G. Elmegreen, Hideaki Furusawa, Kenya Kato, Atsushi Kawai, Yoshinao Kobayashi, Takahiro Koishi, Geoffrey D. McNiven, Tetsu Narumi, Kenji Yasuoka

Research output: Contribution to journalArticlepeer-review

59 Citations (Scopus)


We developed MDGRAPE-2, a hardware accelerator that calculates forces at high speed in molecular dynamics (MD) simulations. MDGRAPE-2 is connected to a PC or a workstation as an extension board. The sustained performance of one MDGRAPE-2 board is 15 Gflops, roughly equivalent to the peak performance of the fastest supercomputer processing element. One board is able to calculate all forces between 10000 particles in 0.28 s (i.e. 310000 time steps per day). If 16 boards are connected to one computer and operated in parallel, this calculation speed becomes ∼ 10 times faster. In addition to MD, MDGRAPE-2 can be applied to gravitational N-body simulations, the vortex method and smoothed particle hydrodynamics in computational fluid dynamics.

Original languageEnglish
Pages (from-to)115-131
Number of pages17
JournalComputer Physics Communications
Issue number2
Publication statusPublished - 2003 Oct 1


  • Molecular dynamics
  • Special purpose computer

ASJC Scopus subject areas

  • Hardware and Architecture
  • General Physics and Astronomy


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