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Title: Implementation of replica-exchange umbrella sampling in GAMESS

Journal Article · · Computer Physics Communications

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. Here, 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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE; Japan Society for the Promotion of Science (JSPS)
Grant/Contract Number:
AC05-00OR22725; JP16H06353; JP25247071; JP25102009
OSTI ID:
1659568
Journal Information:
Computer Physics Communications, Vol. 228, Issue 1; ISSN 0010-4655
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

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Cited By (1)

Protein structure predictions by enhanced conformational sampling methods journal January 2019