Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 35, Issue 5, Pages 406-413Publisher
WILEY-BLACKWELL
DOI: 10.1002/jcc.23501
Keywords
CHARMM; molecular dynamics; parallel programming; domain decomposition
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Funding
- Department of Energy, Office of Advanced Computing Research [SciDAC DE-AC36-99G0-10337]
- NIH [R01 GM103695]
- DOE Office of the Biomass Program
- DOE EERE (NREL Computational Sciences Center) [DE-AC36-08GO28308]
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We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. (c) 2013 Wiley Periodicals, Inc.
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