Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

被引：6

作者：

Myung, Hun Joo ^{[1
]}

Sakamaki, Ryuji ^{[2
]}

Oh, Kwang Jin ^{[1
]}

Narumi, Tetsu ^{[3
]}

Yasuoka, Kenji ^{[2
]}

Lee, Sik ^{[1
]}

机构：

[1] KISTI Supercomp Ctr, Taejon 305806, South Korea

[2] Keio Univ, Dept Mech Engn, Yokohama, Kanagawa 2238522, Japan

[3] Univ Electrocommun, Dept Comp Sci, Tokyo, Japan

来源：

BULLETIN OF THE KOREAN CHEMICAL SOCIETY | 2010年 / 31卷 / 12期

关键词：

Molecular dynamics simulation; Parallel computing; GPU; Biomolecules; MESH EWALD METHOD; CONSTRAINTS; SYSTEM;

D O I：

10.5012/bkcs.2010.31.12.3639

中图分类号：

O6 [化学];

学科分类号：

0703 ;

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.

引用

收藏

页码：3639 / 3643

页数：5

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