title: The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations.
abstract: Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used.
authors.affiliation: National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia.
authors.forename: Urban
authors.initials: U
authors.lastname: Borštnik
authors.forename: Benjamin T
authors.initials: BT
authors.lastname: Miller
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.forename: Dušanka
authors.initials: D
authors.lastname: Janežič
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D012984:Software