Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

作者：Myung Hun Joo; Sakamaki Ryuji; Oh Kwang Jin^*; Narumi Tetsu; Yasuoka Kenji; Lee Sik

来源：Bulletin of the Korean Chemical Society, 2010, 31(12): 3639-3643.

DOI：10.5012/bkcs.2010.31.12.3639

• Molecular dynamics simulation
• Parallel computing
• GPU
• Biomolecules

We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described. Here we have focused on the non-bonded force calculation because it is most time consuming part in molecular dynamics simulation. Timing results using CUDA-enabled and CPU versions were obtained and compared for a biomolecular system-containing 23558 atoms. CUDA-enabled versions were found to be faster than CPU version. This suggests that GPU could be a useful hardware for molecular dynamics simulation.

• 出版日期2010-12-20