Molecular dynamics simulation using graphics processing units

Guoliang Song, Jing Wei Weng, Zhen Hua Li, Wen Ning Wang, Kang Nian Fan

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


In this paper, the molecular dynamics program with CHARMM force field is developed on Graphics processing unit (GPU) at Windows computer cluster server (WCCS) system. From the testing results of peptide chain, the efficiency of GPU is outstanding compared with that of CPU. The efficiency on NVIDIA GeForce 8800 GT GPU is at lease 10 times faster than that on a single Athlon 2.0G CPU. When the total molecule size is enlarged, the number of vacant parallel units in GPU decreases, so the parallel efficiency increases. At the same time, while the fragment size is enlarged, the buffer size of a fragment decreases relatively, so the total efficiency also increases. The maximum efficiency ratio of GPU/CPU reaches to 28 times according to our test. At last, a peptide chain with 397 atoms is tested for simulation and the population of hydrogen bond is described at different time steps.

Original languageEnglish (US)
Pages (from-to)2425-2429
Number of pages5
JournalGaodeng Xuexiao Huaxue Xuebao/Chemical Journal of Chinese Universities
Issue number12
StatePublished - Dec 1 2008


  • Graphics processing unit
  • Molecular dynamics
  • Windows computer cluster server


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