期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 27, 期 6, 页码 719-729出版社
WILEY
DOI: 10.1002/jcc.20387
关键词
molecular surface; generalized Born formalisms; molecular dynamic simulations
Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple SWitching) methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the GBMV method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs. (c) 2006 Wiley Periodicals, Inc.
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