Accelerating molecular dynamics simulation using graphics processing unit

Bulletin of the Korean chemical society

Hun Joo Myung¹  Kenji Yasuoka¹  Sik Lee¹  Kwang Jin Oh¹  Tetsu Narumi¹  Ryuji Sakamaki¹ 

关键词: Molecular dynamics simulation;    Parallel computing;    GPU;    Biomolecules;   

DOI  :  

学科分类：化学（综合）

来源: Korean Chemical Society

【 摘 要 】

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.

【 授权许可】

Unknown