期刊
COMPUTER PHYSICS COMMUNICATIONS
卷 228, 期 -, 页码 152-162出版社
ELSEVIER
DOI: 10.1016/j.cpc.2018.01.014
关键词
Replica-exchange molecular dynamics; Multidimensional replica-exchange method; Umbrella sampling; Replica-exchange umbrella sampling; Density-functional tight-binding; GAMESS-US
资金
- [JP16H06353]
- [JP25247071]
- [JP25102009]
In GAMESS-US quantum chemistry package, both replica-exchange molecular dynamics (REMD) and the umbrella sampling (US) methods are available. However, prior to this work, the replica-exchange umbrella sampling (REUS) method, combining REMD and US, was not implemented. REUS affords a more efficient conformational sampling than the conventional US method and is often used in MD simulations. We implemented REUS in GAMESS-US and improved some routines of the existing REMD code. A density-functional tight-binding REMD (DFTB-REMD) simulation of alanine deca-peptide and a DFTB-MD REUS simulation of proton transfer in malonaldehyde were performed. The results of DFTB-MD REUS simulations performed with three different simulation packages were compared to validate our GAMESS-US implementation. (C) 2018 Published by Elsevier B.V.
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