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 (全般)