title: Implementation of the force decomposition machine for molecular dynamics simulations.
abstract: We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect.
authors.affiliation: National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, 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; D016333:HIV Protease / Q000737:chemistry*; D015497:HIV-1 / Q000737:chemistry / Q000201:enzymology; D006801:Humans; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D016571:Neural Networks, Computer; D060388:Support Vector Machine
chemical_list: D009211:Myoglobin; C018013:carboxymyoglobin; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1