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http://dx.doi.org/10.5012/bkcs.2010.31.12.3639

Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit  

Myung, Hun-Joo (KISTI Supercomputing Center)
Sakamaki, Ryuji (Department of Mechanical Engineering, Keio University)
Oh, Kwang-Jin (KISTI Supercomputing Center)
Narumi, Tetsu (Department of Computer Science, University of Electro-Communications)
Yasuoka, Kenji (Department of Mechanical Engineering, Keio University)
Lee, Sik (KISTI Supercomputing Center)
Publication Information
Bulletin of the Korean Chemical Society / v.31, no.12, 2010 , pp. 3639-3643 More about this Journal
Abstract
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.
Keywords
Molecular dynamics simulation; Parallel computing; GPU; Biomolecules;
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