Molecular dynamics simulation using graphics processing units

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.