Implementation of replica-exchange umbrella sampling in GAMESS

Ito, Shingo; Fedorov, Dmitri G.; Okamoto, Yuko; Irle, Stephan

doi:10.1016/j.cpc.2018.01.014

Title: Implementation of replica-exchange umbrella sampling in GAMESS

Journal Article · Sun Jul 01 00:00:00 EDT 2018 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2018.01.014· OSTI ID:1659568

Ito, Shingo ^[1];

^[2]; Okamoto, Yuko ^[1];

^[1]

Nagoya Univ. (Japan)
National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)

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.

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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

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Cited by: 6 works

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Title: Implementation of replica-exchange umbrella sampling in GAMESS

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