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Scientific Programming
Volume 8 (2000), Issue 3, Pages 195-207

Scalable Molecular Dynamics for Large Biomolecular Systems

Robert K. Brunner,1 James C. Phillips,1 and Laxmikant V. Kalé2

1Theoretical Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Received 26 June 2001; Accepted 26 June 2001

Copyright © 2000 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.