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.
|Number of pages||5|
|Journal||Bulletin of the Korean Chemical Society|
|Publication status||Published - 2010 Dec 20|
- Molecular dynamics simulation
- Parallel computing
ASJC Scopus subject areas