A new dynamical domain decomposition method for parallel molecular dynamics simulation

A new material particle dynamical domain decomposition method MPD³ has been developed. The method is suitable for a large scale parallel molecular dynamic simulation on a heterogeneous computing net. Performance of the MPD³ algorithm is tested in various computing environments, such as PC clusters, super computer clusters, and grid. It is shown that the MPD³ algorithm is highly-adaptive for both computer clusters and grid computing environments, even if other programs are running on the same computer environment.