Scalable Molecular Dynamics for Large Biomolecular Systems

R.K. Brunner, J.C. Phillips, L.V. Kale
<span title="">2000</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="" style="color: black;">ACM/IEEE SC 2000 Conference (SC&#39;00)</a> </i> &nbsp;
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
more &raquo; ... ic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations. 0-7803-9802-5/2000/$10.00 (c) 2000 IEEE.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1109/sc.2000.10038</a> <a target="_blank" rel="external noopener" href="">dblp:conf/sc/BrunnerPK00</a> <a target="_blank" rel="external noopener" href="">fatcat:hyhy6i3czfhcrksqh4hltj2bqi</a> </span>
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