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

Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka

研究成果: Chapter

抄録

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.

本文言語English
ホスト出版物のタイトルMolecular Simulation in Material and Biological Research
出版社Nova Science Publishers, Inc.
ページ29-40
ページ数12
ISBN(印刷版)9781607415534
出版ステータスPublished - 2009 12月 1

ASJC Scopus subject areas

  • 化学一般
  • 生化学、遺伝学、分子生物学一般

フィンガープリント

「Using special-Purpose and video-game computers for accelerating molecular dynamics simulations」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル