Parallelizing molecular dynamics programs for distributed-memory machines

Abstract

Using a data-parallel strategy to parallelize molecular dynamics programs makes it possible to simulate very large molecules on large numbers of processors. Applying on appropriate combination of data partitioning and iteration distribution algorithms not only optimizes communication overheads but also achieves good load balance, and hence good performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>