Accelerating molecular dynamics simulation using graphics processing unit

Hun Joo Myung, Ryuji Sakamaki, Kwang Jin Oh, Tetsu Narumi, Kenji Yasuoka, Sik Lee

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3639-3643
Number of pages5
JournalBulletin of the Korean Chemical Society
Volume31
Issue number12
DOIs
Publication statusPublished - 2010 Dec 20

Keywords

  • Biomolecules
  • GPU
  • Molecular dynamics simulation
  • Parallel computing

ASJC Scopus subject areas

  • Chemistry(all)

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