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

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.