期刊
COMPUTER PHYSICS COMMUNICATIONS
卷 204, 期 -, 页码 1-10出版社
ELSEVIER
DOI: 10.1016/j.cpc.2016.02.010
关键词
Replica-exchange molecular dynamics; Multidimensional replica-exchange method; Umbrella sampling; Replica-exchange umbrella sampling; Density functional tight binding; DFTB; Malonaldehyde; Phthalocyanine
资金
- Program for Leading Graduate Schools Integrative Graduate Education and Research in Green Natural Sciences of Nagoya University
- JSPS [25247071]
- MEXT, Japan
- Grants-in-Aid for Scientific Research [25102009, 26410013, 25102001, 25247071] Funding Source: KAKEN
The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB+ quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB+ combination. (C) 2016 Published by Elsevier B.V.
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