Automated Exploration of Free Energy Landscapes Based on Umbrella Integration

We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We app...

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Detalles Bibliográficos
Autores principales: Mitsuta, Yuki, Kawakami, Takashi, Okumura, Mitsutaka, Yamanaka, Shusuke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979611/
https://www.ncbi.nlm.nih.gov/pubmed/29561821
http://dx.doi.org/10.3390/ijms19040937
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author Mitsuta, Yuki
Kawakami, Takashi
Okumura, Mitsutaka
Yamanaka, Shusuke
author_facet Mitsuta, Yuki
Kawakami, Takashi
Okumura, Mitsutaka
Yamanaka, Shusuke
author_sort Mitsuta, Yuki
collection PubMed
description We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values.
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spelling pubmed-59796112018-06-10 Automated Exploration of Free Energy Landscapes Based on Umbrella Integration Mitsuta, Yuki Kawakami, Takashi Okumura, Mitsutaka Yamanaka, Shusuke Int J Mol Sci Article We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values. MDPI 2018-03-21 /pmc/articles/PMC5979611/ /pubmed/29561821 http://dx.doi.org/10.3390/ijms19040937 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Mitsuta, Yuki
Kawakami, Takashi
Okumura, Mitsutaka
Yamanaka, Shusuke
Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_full Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_fullStr Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_full_unstemmed Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_short Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_sort automated exploration of free energy landscapes based on umbrella integration
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979611/
https://www.ncbi.nlm.nih.gov/pubmed/29561821
http://dx.doi.org/10.3390/ijms19040937
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AT okumuramitsutaka automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration
AT yamanakashusuke automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration

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