Using special-Purpose and video-game computers for accelerating molecular dynamics simulations

Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIAs Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. We compared performances of gravitational Af-body and MD simulations with four hardware: CPU (dual Intel Xeon E5430), PS3, GPU (NVIDIA GeForce9800GTX), and MDGRAPE-3. As for gravitational N-body simulation, the GPU is the fastest and almost best in also other criteria: cost/performance, power/performance, and size/performance. For MD simulation with AMBER MD package, the MDGRAPE-3 is the fastest and the best for power/performance, while the PS3 is the best for cost/performance.

Original languageEnglish
Title of host publicationMolecular Simulation in Material and Biological Research
PublisherNova Science Publishers, Inc.
Pages29-40
Number of pages12
ISBN (Print)9781607415534
Publication statusPublished - 2009

Fingerprint

Video Games
Computer games
Molecular Dynamics Simulation
Molecular dynamics
Computer simulation
Computer hardware
Program processors
Costs and Cost Analysis
Van der Waals forces
Cost effectiveness
Cost-Benefit Analysis
Costs
Atoms
Graphics processing unit

Keywords

  • Grape
  • Graphics processing unit
  • Molecular dynamics simulation
  • Playstation 3
  • Special-purpose computer

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Narumi, T., Sakamaki, R., Kameoka, S., & Yasuoka, K. (2009). Using special-Purpose and video-game computers for accelerating molecular dynamics simulations. In Molecular Simulation in Material and Biological Research (pp. 29-40). Nova Science Publishers, Inc..

Using special-Purpose and video-game computers for accelerating molecular dynamics simulations. / Narumi, Tetsu; Sakamaki, Ryuji; Kameoka, Shun; Yasuoka, Kenji.

Molecular Simulation in Material and Biological Research. Nova Science Publishers, Inc., 2009. p. 29-40.

Research output: Chapter in Book/Report/Conference proceedingChapter

Narumi, T, Sakamaki, R, Kameoka, S & Yasuoka, K 2009, Using special-Purpose and video-game computers for accelerating molecular dynamics simulations. in Molecular Simulation in Material and Biological Research. Nova Science Publishers, Inc., pp. 29-40.
Narumi T, Sakamaki R, Kameoka S, Yasuoka K. Using special-Purpose and video-game computers for accelerating molecular dynamics simulations. In Molecular Simulation in Material and Biological Research. Nova Science Publishers, Inc. 2009. p. 29-40
Narumi, Tetsu ; Sakamaki, Ryuji ; Kameoka, Shun ; Yasuoka, Kenji. / Using special-Purpose and video-game computers for accelerating molecular dynamics simulations. Molecular Simulation in Material and Biological Research. Nova Science Publishers, Inc., 2009. pp. 29-40
@inbook{30a188ca03d04f8ca83e39ffe1d3a2df,
title = "Using special-Purpose and video-game computers for accelerating molecular dynamics simulations",
abstract = "Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIAs Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. We compared performances of gravitational Af-body and MD simulations with four hardware: CPU (dual Intel Xeon E5430), PS3, GPU (NVIDIA GeForce9800GTX), and MDGRAPE-3. As for gravitational N-body simulation, the GPU is the fastest and almost best in also other criteria: cost/performance, power/performance, and size/performance. For MD simulation with AMBER MD package, the MDGRAPE-3 is the fastest and the best for power/performance, while the PS3 is the best for cost/performance.",
keywords = "Grape, Graphics processing unit, Molecular dynamics simulation, Playstation 3, Special-purpose computer",
author = "Tetsu Narumi and Ryuji Sakamaki and Shun Kameoka and Kenji Yasuoka",
year = "2009",
language = "English",
isbn = "9781607415534",
pages = "29--40",
booktitle = "Molecular Simulation in Material and Biological Research",
publisher = "Nova Science Publishers, Inc.",

}

TY - CHAP

T1 - Using special-Purpose and video-game computers for accelerating molecular dynamics simulations

AU - Narumi, Tetsu

AU - Sakamaki, Ryuji

AU - Kameoka, Shun

AU - Yasuoka, Kenji

PY - 2009

Y1 - 2009

N2 - Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIAs Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. We compared performances of gravitational Af-body and MD simulations with four hardware: CPU (dual Intel Xeon E5430), PS3, GPU (NVIDIA GeForce9800GTX), and MDGRAPE-3. As for gravitational N-body simulation, the GPU is the fastest and almost best in also other criteria: cost/performance, power/performance, and size/performance. For MD simulation with AMBER MD package, the MDGRAPE-3 is the fastest and the best for power/performance, while the PS3 is the best for cost/performance.

AB - Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIAs Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. We compared performances of gravitational Af-body and MD simulations with four hardware: CPU (dual Intel Xeon E5430), PS3, GPU (NVIDIA GeForce9800GTX), and MDGRAPE-3. As for gravitational N-body simulation, the GPU is the fastest and almost best in also other criteria: cost/performance, power/performance, and size/performance. For MD simulation with AMBER MD package, the MDGRAPE-3 is the fastest and the best for power/performance, while the PS3 is the best for cost/performance.

KW - Grape

KW - Graphics processing unit

KW - Molecular dynamics simulation

KW - Playstation 3

KW - Special-purpose computer

UR - http://www.scopus.com/inward/record.url?scp=84895202930&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84895202930&partnerID=8YFLogxK

M3 - Chapter

AN - SCOPUS:84895202930

SN - 9781607415534

SP - 29

EP - 40

BT - Molecular Simulation in Material and Biological Research

PB - Nova Science Publishers, Inc.

ER -