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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Main Authors:	Yuki Mitsuta, Takashi Kawakami, Mitsutaka Okumura, Shusuke Yamanaka
Format:	Article
Language:	English
Published:	MDPI AG 2018-03-01
Series:	International Journal of Molecular Sciences
Subjects:	automated search potential of mean force umbrella integration
Online Access:	http://www.mdpi.com/1422-0067/19/4/937

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record_format	Article
spelling	doaj-87df893eeb444a27a481492f8b859b5f2020-11-25T01:05:34ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-03-0119493710.3390/ijms19040937ijms19040937Automated Exploration of Free Energy Landscapes Based on Umbrella IntegrationYuki Mitsuta0Takashi Kawakami1Mitsutaka Okumura2Shusuke Yamanaka3Graduate School of Science, Osaka University, Osaka 565-0871, JapanGraduate School of Science, Osaka University, Osaka 565-0871, JapanGraduate School of Science, Osaka University, Osaka 565-0871, JapanGraduate School of Science, Osaka University, Osaka 565-0871, JapanWe 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.http://www.mdpi.com/1422-0067/19/4/937automated searchpotential of mean forceumbrella integration
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Yuki Mitsuta Takashi Kawakami Mitsutaka Okumura Shusuke Yamanaka
spellingShingle	Yuki Mitsuta Takashi Kawakami Mitsutaka Okumura Shusuke Yamanaka Automated Exploration of Free Energy Landscapes Based on Umbrella Integration International Journal of Molecular Sciences automated search potential of mean force umbrella integration
author_facet	Yuki Mitsuta Takashi Kawakami Mitsutaka Okumura Shusuke Yamanaka
author_sort	Yuki Mitsuta
title	Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
title_short	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_sort	automated exploration of free energy landscapes based on umbrella integration
publisher	MDPI AG
series	International Journal of Molecular Sciences
issn	1422-0067
publishDate	2018-03-01
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.
topic	automated search potential of mean force umbrella integration
url	http://www.mdpi.com/1422-0067/19/4/937
work_keys_str_mv	AT yukimitsuta automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration AT takashikawakami automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration AT mitsutakaokumura automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration AT shusukeyamanaka automatedexplorationoffreeenergylandscapesbasedonumbrellaintegration
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Automated Exploration of Free Energy Landscapes Based on Umbrella Integration

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