New faster CHARMM molecular dynamics engine

Antti-Pekka Hynninen; Michael F Crowley

doi:10.1002/jcc.23501

New faster CHARMM molecular dynamics engine

J Comput Chem. 2014 Feb 15;35(5):406-13. doi: 10.1002/jcc.23501. Epub 2013 Dec 2.

Authors

Antti-Pekka Hynninen¹, Michael F Crowley

Affiliation

¹ Computational Science Center, National Renewable Energy Laboratory, Golden, Colorado, 80401.

Abstract

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.

Keywords: CHARMM; domain decomposition; molecular dynamics; parallel programming.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Molecular Dynamics Simulation*
Software*
Time Factors

Grants and funding

R01 GM103695/GM/NIGMS NIH HHS/United States