Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit
HJ Myung and R Sakamaki and KJ Oh and T Narumi and K Yasuoka and S Lee, BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 31, 3639-3643 (2010).
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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