New decomposition strategy for parallel bonded molecular dynamics

摘要

A method is described for parallelizing molecular dynamics (MD) simulations by block-decomposing the matrix of bonded and non-bonded force computations. It is particularly useful for organic simulations (polymers, proteins) because unlike spatial-decomposition methods, it requires no geometric information about the simulation domain. Because its communication cost scales as N/(radical)P. rather than N as in the all-to-all broadcast or ring-exchange techniques commonly used in this type of MD simulation, larger numbers of processors can be used effectively, yielding greater parallel speed-ups.