A mixed geometric-systolic approach to parallel molecular dynamics simulations Original Research Article

We have developed a flexible and efficient method of performing molecular dynamics simulations on distributed memory parallel computers. The novel feature is to use simultaneously spatial partitioning and systolic loop approaches according to a strategy which, for a given simulation, adapts itself to the multiprocessor system, allowing to approach optimal performance. The method assures high efficiencies even in situations in which, due to the exceeding large number of processors, the usage of a pure spatial decomposition would be impossible. The algorithm provides as particular cases both the pure spatial partitioning and the pure systolic parallelization schemes, so that its adoption assures maximum flexibility.