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Title: Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

Abstract

Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.

Authors:
ORCiD logo [1];  [2]
  1. Argonne National Lab. (ANL), Argonne, IL (United States)
  2. Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Institutes of Health (NIH)
OSTI Identifier:
1374573
Grant/Contract Number:  
AC02-06CH11357; U54-GM087519
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 145; Journal Issue: 13; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; constant pH; expanded ensemble; linear response; nonequilibrium MD/MC

Citation Formats

Radak, Brian K., and Roux, Benoît. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations. United States: N. p., 2016. Web. doi:10.1063/1.4964288.
Radak, Brian K., & Roux, Benoît. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations. United States. doi:10.1063/1.4964288.
Radak, Brian K., and Roux, Benoît. Fri . "Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations". United States. doi:10.1063/1.4964288. https://www.osti.gov/servlets/purl/1374573.
@article{osti_1374573,
title = {Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations},
author = {Radak, Brian K. and Roux, Benoît},
abstractNote = {Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.},
doi = {10.1063/1.4964288},
journal = {Journal of Chemical Physics},
number = 13,
volume = 145,
place = {United States},
year = {Fri Oct 07 00:00:00 EDT 2016},
month = {Fri Oct 07 00:00:00 EDT 2016}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 4 works
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Works referenced in this record:

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289