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A Special-purpose Computer for Molecular Dynamics Simulations: MDM

Published online by Cambridge University Press:  26 May 2016

Tetsu Narumi
Tetsu Narumi*
Affiliation:
High Performance Biocomputing Team, Computer/Informatics Facilities, RIKEN Genomic Sciences Center, Maeda 214, Totsuka, Yokohama, Kanagawa 244-0408, Japan

Abstract

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We developed a special-purpose computer for molecular dynamics simulations, which we call Molecular Dynamics Machine (MDM). MDM accelerates the Coulomb and van der Waals force calculation with the Ewald method. It is composed of three parts: MDGRAPE-2, WINE-2 and a host computer. MDGRAPE-2 accelerates the real-space part of the Coulomb and van der Waals forces. WINE-2 accelerates wavenumber-space part of the Coulomb force. The host computer performs other calculations. The peak performance is 78 Tflop/s. It can also be used for cosmological, Smoothed Particle Hydrodynamics, and vortex dynamics simulations.

Type
Hardware and Software Environments
Information
Symposium - International Astronomical Union , Volume 208: Astrophysical Supercomputing using Particle Simulations , 2003 , pp. 349 - 358
Copyright
Copyright © Astronomical Society of the Pacific 2003 

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