Dissipative particle dynamics (DPD) is a new promising method commonly used in coarse-grained simulations of soft matter and biomolecular systems at constant temperature. The DPD thermostat involves the evaluation of stochastic or random forces between pairs of neighboring particles in every time step. In a parallel computing environment, the transfer of these forces from node to node can be very time consuming. In this paper we describe the implementation of a seeded random number generator with three input seeds at each step which enables the complete generation of the pairwise stochastic forces in parallel DPD simulations with minimal communication between nodes.
Bibliographical noteFunding Information:
Y. Afshar was a recipient of a fellowship of the Graduate School Materials Science in Mainz (MAINZ) funded through the German Research Foundation in the Excellence Initiative (GSC 266). Additionally, Y. Afshar would like to thank Dr. Michael Seaton (Computational Chemistry Group, Daresbury Laboratory) for useful discussion regarding the standard method implementation.
Copyright 2013 Elsevier B.V., All rights reserved.
- Dissipative particle dynamics
- Domain decomposition
- Parallel computing
- Random number generator