@inproceedings{4ec51ce24cee42649220ab55206c7d2f,
title = "Scalable molecular dynamics for large biomolecular systems",
abstract = "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.",
author = "Brunner, {Robert K.} and Phillips, {James C.} and Kal{\'e}, {Laxmikant V.}",
note = "Publisher Copyright: {\textcopyright} 2000 IEEE.; 2000 ACM/IEEE Conference on Supercomputing, SC 2000 ; Conference date: 04-11-2000 Through 10-11-2000",
year = "2000",
doi = "10.1109/SC.2000.10038",
language = "English (US)",
series = "Proceedings of the International Conference on Supercomputing",
publisher = "Association for Computing Machinery",
booktitle = "SC 2000 - Proceedings of the 2000 ACM/IEEE Conference on Supercomputing",
address = "United States",
}