Evaluating Parallel Languages for Molecular Dynamics Computations

Computational molecular dynamics is an important application requiring large amounts of computing time. Parallel processing ooers the possibility of much better performance on scientiic computation, but irregular problems like molecular dynamics have proven dif-cult to map onto parallel machines. In this paper, we describe the practicalities of porting a basic molecular dynamics computation to a distributed-memory machine. In the process, we show how program annotations can aid in parallelizing a moderately complex code. We also argue that algorithm replacement may be necessary in parallelization, a task which cannot be performed automatically. We close with some results from a parallel GROMOS implementation.