title: Improving the performance of molecular dynamics simulations on parallel clusters.
abstract: In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds.
authors.affiliation: National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
authors.forename: Urban
authors.initials: U
authors.lastname: Borstnik
authors.forename: Milan
authors.initials: M
authors.lastname: Hodoscek
authors.forename: Dusanka
authors.initials: D
authors.lastname: Janezic