Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

Radak, Brian K.; Roux, Benoît

doi:10.1063/1.4964288

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

Journal Article · Fri Oct 07 00:00:00 EDT 2016 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4964288· OSTI ID:1374573

^[1]; Roux, Benoît ^[2]

Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials

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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1374573

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 13 Vol. 145; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe The Journal of Chemical Physics, Vol. 148, Issue 1 https://doi.org/10.1063/1.5004154	journal	January 2018
A generalized linear response framework for expanded ensemble and replica exchange simulations Radak, Brian K.; Suh, Donghyuk; Roux, Benoît The Journal of Chemical Physics, Vol. 149, Issue 7 https://doi.org/10.1063/1.5027494	journal	August 2018
Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches Procacci, Piero The Journal of Chemical Physics, Vol. 151, Issue 14 https://doi.org/10.1063/1.5120615	journal	October 2019
Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates Procacci, Piero The Journal of Chemical Physics, Vol. 151, Issue 14 https://doi.org/10.1063/1.5120616	journal	October 2019

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