NAMD: Biomolecular simulation on thousands of processors

James C. Phillips, Gengbin Zheng, Sameer Kumar, Laxmikant V. Kalé

Research output: Chapter in Book/Report/Conference proceedingConference contribution


NAMD is a fully featured, production molecular dynamics program for high performance simulation of large biomolecular systems. We have previously, at SC2000, presented scaling results for simulations with cutoff electrostatics on up to 2048 processors of the ASCI Red machine, achieved with an object-based hybrid force and spatial decomposition scheme and an aggressive measurement-based predictive load balancing framework. We extend this work by demonstrating similar scaling on the much faster processors of the PSC Lemieux Alpha cluster, and for simulations employing efficient (order N log N) particle mesh Ewald full electrostatics. This unprecedented scalability in a biomolecular simulation code has been attained through latency tolerance, adaptation to multiprocessor nodes, and the direct use of the Quadrics Elan library in place of MPI by the Charm++/Converse parallel runtime system.

Original languageEnglish (US)
Title of host publicationProceedings of the IEEE/ACM SC 2002 Conference, SC 2002
PublisherAssociation for Computing Machinery
ISBN (Electronic)076951524X
StatePublished - 2002
Event2002 IEEE/ACM Conference on Supercomputing, SC 2002 - Baltimore, United States
Duration: Nov 16 2002Nov 22 2002

Publication series

NameProceedings of the International Conference on Supercomputing


Conference2002 IEEE/ACM Conference on Supercomputing, SC 2002
Country/TerritoryUnited States

ASJC Scopus subject areas

  • Computer Science(all)


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