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Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations

[Image: see text] We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations,...

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Autores principales: Moradi, Mahmoud, Tajkhorshid, Emad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2013
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688312/
https://www.ncbi.nlm.nih.gov/pubmed/23795244
http://dx.doi.org/10.1021/jz400816x
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author Moradi, Mahmoud
Tajkhorshid, Emad
author_facet Moradi, Mahmoud
Tajkhorshid, Emad
author_sort Moradi, Mahmoud
collection PubMed
description [Image: see text] We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.
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spelling pubmed-36883122013-06-21 Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations Moradi, Mahmoud Tajkhorshid, Emad J Phys Chem Lett [Image: see text] We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation. American Chemical Society 2013-05-17 2013-06-06 /pmc/articles/PMC3688312/ /pubmed/23795244 http://dx.doi.org/10.1021/jz400816x Text en Copyright © 2013 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html)
spellingShingle Moradi, Mahmoud
Tajkhorshid, Emad
Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title_full Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title_fullStr Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title_full_unstemmed Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title_short Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
title_sort driven metadynamics: reconstructing equilibrium free energies from driven adaptive-bias simulations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688312/
https://www.ncbi.nlm.nih.gov/pubmed/23795244
http://dx.doi.org/10.1021/jz400816x
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