期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 35, 期 1, 页码 39-50出版社
WILEY
DOI: 10.1002/jcc.23462
关键词
generalized ensemble method; partial system; free energy landscape; explicit water; all-atom model
资金
- Ministry of Education, Culture, Sports, Science and Technology in Japan [23114723]
- MEXT Strategic Programs for Innovative Research, Computational Life Science and Application in Drug Discovery and Medical Development
- Grants-in-Aid for Scientific Research [25116003] Funding Source: KAKEN
A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. (c) 2013 Wiley Periodicals, Inc.
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