Abstract
We have developed a new program named Parallel Molecular Dynamics Stencil, which is an integrated assembly of simulation techniques for executing molecular dynamics in a parallel computing environment. The Stencil is designed in such a way to conceal parts of the programs for parallelization. With the Stencil’s framework, parallel programming for force calculation can be done in the same way as sequential programming. So, it can be easily adapted to employed physical models. It is shown that the performance of the Stencil is excellent by choosing the combination of the spatial decomposition and the cell partitioning methods.
