Large-Scale Molecular Dynamics Simulations on Parallel Clusters

We have developed a parallel program for molecular dynamics (MD) simulation on clusters of personal computers (PCs). The program implements the Split Integration Symplectic Method (SISM) for MD integration that analytically treats high-frequency motions in molecules, allowing the simulation time step to be longer than in standard methods. The program is designed to run on parallel clusters of personal computers that we have built. Additionally, MD-GRAPE II processors, which are designed for fast MD simulations, can be used to calculate nonbonding interactions among atoms. Multiple such processors can be used in parallel, further reducing the computational time. We have compared the performance of the implemented program with several different numbers of processors using two different-sized molecular systems. The parallelization of the SISM and the use of the MD-GRAPE II is shown to be an effective combination.