A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity Original Research Article

We describe in this paper methods for applying domain decomposition to a general purpose molecular dynamics program. The algorithm is suitable for either distributed memory parallel computers or shared memory machines with message passing libraries. A method is discussed in detail which allows molecules of arbitrary connectivity to be simulated within the domain decomposition approach. The algorithm also contains techniques to handle both rigid bond constraints and special CH2 constraints which involve five atoms. Examples are given for molecular systems containing both types of constraints plus two, three- and four-body intramolecular potentials as well as short-range and long-range non-bonded potentials. The algorithm has been implemented on a Silicon Graphics Power Challenge machine using the MPI message passing library.