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Title: Implementation of replica-exchange umbrella sampling in GAMESS

Abstract

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.

Authors:
 [1]; ORCiD logo [2];  [1]; ORCiD logo [1]
  1. Nagoya Univ. (Japan)
  2. National Inst. of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; Japan Society for the Promotion of Science (JSPS)
OSTI Identifier:
1659568
Grant/Contract Number:  
AC05-00OR22725; JP16H06353; JP25247071; JP25102009
Resource Type:
Accepted Manuscript
Journal Name:
Computer Physics Communications
Additional Journal Information:
Journal Volume: 228; Journal Issue: 1; Journal ID: ISSN 0010-4655
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; density-functional tight-binding; GAMESS-US; multidimensional replica-exchange method; replica-exchange molecular dynamics; replica-exchange umbrella sampling; umbrella sampling

Citation Formats

Ito, Shingo, Fedorov, Dmitri G., Okamoto, Yuko, and Irle, Stephan. Implementation of replica-exchange umbrella sampling in GAMESS. United States: N. p., 2018. Web. doi:10.1016/j.cpc.2018.01.014.
Ito, Shingo, Fedorov, Dmitri G., Okamoto, Yuko, & Irle, Stephan. Implementation of replica-exchange umbrella sampling in GAMESS. United States. https://doi.org/10.1016/j.cpc.2018.01.014
Ito, Shingo, Fedorov, Dmitri G., Okamoto, Yuko, and Irle, Stephan. Sun . "Implementation of replica-exchange umbrella sampling in GAMESS". United States. https://doi.org/10.1016/j.cpc.2018.01.014. https://www.osti.gov/servlets/purl/1659568.
@article{osti_1659568,
title = {Implementation of replica-exchange umbrella sampling in GAMESS},
author = {Ito, Shingo and Fedorov, Dmitri G. and Okamoto, Yuko and Irle, Stephan},
abstractNote = {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.},
doi = {10.1016/j.cpc.2018.01.014},
journal = {Computer Physics Communications},
number = 1,
volume = 228,
place = {United States},
year = {Sun Jul 01 00:00:00 EDT 2018},
month = {Sun Jul 01 00:00:00 EDT 2018}
}

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Works referencing / citing this record:

Protein structure predictions by enhanced conformational sampling methods
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