w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

[Image: see text] Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy...

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Autores principales: Arrar, Mehrnoosh, de Oliveira, Cesar Augusto F., Fajer, Mikolai, Sinko, William, McCammon, J. Andrew
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2012
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541756/
https://www.ncbi.nlm.nih.gov/pubmed/23316122
http://dx.doi.org/10.1021/ct300896h
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author Arrar, Mehrnoosh
de Oliveira, Cesar Augusto F.
Fajer, Mikolai
Sinko, William
McCammon, J. Andrew
author_facet Arrar, Mehrnoosh
de Oliveira, Cesar Augusto F.
Fajer, Mikolai
Sinko, William
McCammon, J. Andrew
author_sort Arrar, Mehrnoosh
collection PubMed
description [Image: see text] Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange framework (w-REXAMD). We show that for a case in which multiple conformations are separated by large free energy barriers, w-REXAMD is a useful enhanced sampling technique, without any necessary reweighting.
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spelling pubmed-35417562013-01-11 w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations Arrar, Mehrnoosh de Oliveira, Cesar Augusto F. Fajer, Mikolai Sinko, William McCammon, J. Andrew J Chem Theory Comput [Image: see text] Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD within a Hamiltonian replica exchange framework (w-REXAMD). We show that for a case in which multiple conformations are separated by large free energy barriers, w-REXAMD is a useful enhanced sampling technique, without any necessary reweighting. American Chemical Society 2012-12-03 2013-01-08 /pmc/articles/PMC3541756/ /pubmed/23316122 http://dx.doi.org/10.1021/ct300896h Text en Copyright © 2012 American Chemical Society http://pubs.acs.org This is an open-access article distributed under the ACS AuthorChoice Terms & Conditions. Any use of this article, must conform to the terms of that license which are available at http://pubs.acs.org.
spellingShingle Arrar, Mehrnoosh
de Oliveira, Cesar Augusto F.
Fajer, Mikolai
Sinko, William
McCammon, J. Andrew
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title_full w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title_fullStr w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title_full_unstemmed w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title_short w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
title_sort w-rexamd: a hamiltonian replica exchange approach to improve free energy calculations for systems with kinetically trapped conformations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541756/
https://www.ncbi.nlm.nih.gov/pubmed/23316122
http://dx.doi.org/10.1021/ct300896h
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