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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 31, Number 12
BKCSDE 31(12)
December 20, 2010 

Accelerating molecular dynamics simulation using graphics processing unit
Hun Joo Myung, Ryuji Sakamaki, Kwang Jin Oh*, Tetsu Narumi, Kenji Yasuoka*, Sik Lee
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.
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