Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

  • Received : 2010.07.16
  • Accepted : 2019.10.06
  • Published : 2010.12.20
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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.

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