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


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.

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.
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


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