title: The midpoint method for parallelization of particle simulations.
abstract: The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.
authors.affiliation: D. E. Shaw Research, LLC, 39th Floor, Tower 45, 120 West 45th Street, New York, New York 10036, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Bowers
authors.forename: Ron O
authors.initials: RO
authors.lastname: Dror
authors.forename: David E
authors.initials: DE
authors.lastname: Shaw
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
chemical_list: D046911:Macromolecular Substances; D012997:Solvents