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Medientyp:
E-Artikel
Titel:
Scalable Molecular Dynamics for Large Biomolecular Systems
Beteiligte:
Brunner, Robert K.;
Phillips, James C.;
Kalé, Laxmikant V.
Erschienen:
Wiley, 2000
Erschienen in:
Scientific Programming, 8 (2000) 3, Seite 195-207
Sprache:
Englisch
DOI:
10.1155/2000/750827
ISSN:
1875-919X;
1058-9244
Entstehung:
Anmerkungen:
Beschreibung:
We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production‐quality molecular dynamics program NAMD. With an object‐based hybrid force and spatial decomposition scheme, and an aggressive measurement‐based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.