A DOMAIN DECOMPOSITION PARALLEL-PROCESSING ALGORITHM FOR MOLECULAR-DYNAMICS SIMULATIONS OF SYSTEMS OF ARBITRARY CONNECTIVITY

We describe in this paper methods for applying domain decomposition to a general purpose molecular dynamics program. The algorithm is suitab le for either distributed memory parallel computers or shared memory m achines with message passing libraries. A method is discussed in detai l which allows molecules of arbitrary connectivity to be simulated wit hin the domain decomposition approach. The algorithm also contains tec hniques to handle both rigid bond constraints and special CH2 constrai nts which involve five atoms. Examples are given for molecular systems containing both types of constraints plus two, three-and four-body in tramolecular potentials as well as short-range and long-range non-bond ed potentials. The algorithm has been implemented on a Silicon Graphic s Power Challenge machine using the MPI message passing library. (C) 1 997 Elsevier Science B.V.