Sciweavers

SC
2000
ACM

Scalable Molecular Dynamics for Large Biomolecular Systems

13 years 9 months ago
Scalable Molecular Dynamics for Large Biomolecular Systems
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.
Robert Brunner, James C. Phillips, Laxmikant V. Ka
Added 01 Aug 2010
Updated 01 Aug 2010
Type Conference
Year 2000
Where SC
Authors Robert Brunner, James C. Phillips, Laxmikant V. Kalé
Comments (0)