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Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression
[Image: see text] The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased densit...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2015
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894281/ https://www.ncbi.nlm.nih.gov/pubmed/26574437 http://dx.doi.org/10.1021/ct501130r |
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author | Meng, Yilin Roux, Benoît |
author_facet | Meng, Yilin Roux, Benoît |
author_sort | Meng, Yilin |
collection | PubMed |
description | [Image: see text] The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. |
format | Online Article Text |
id | pubmed-4894281 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-48942812016-06-25 Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression Meng, Yilin Roux, Benoît J Chem Theory Comput [Image: see text] The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. American Chemical Society 2015-06-25 2015-08-11 /pmc/articles/PMC4894281/ /pubmed/26574437 http://dx.doi.org/10.1021/ct501130r Text en Copyright © 2015 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Meng, Yilin Roux, Benoît Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression |
title | Efficient
Determination of Free Energy Landscapes
in Multiple Dimensions from Biased Umbrella Sampling Simulations Using
Linear Regression |
title_full | Efficient
Determination of Free Energy Landscapes
in Multiple Dimensions from Biased Umbrella Sampling Simulations Using
Linear Regression |
title_fullStr | Efficient
Determination of Free Energy Landscapes
in Multiple Dimensions from Biased Umbrella Sampling Simulations Using
Linear Regression |
title_full_unstemmed | Efficient
Determination of Free Energy Landscapes
in Multiple Dimensions from Biased Umbrella Sampling Simulations Using
Linear Regression |
title_short | Efficient
Determination of Free Energy Landscapes
in Multiple Dimensions from Biased Umbrella Sampling Simulations Using
Linear Regression |
title_sort | efficient
determination of free energy landscapes
in multiple dimensions from biased umbrella sampling simulations using
linear regression |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894281/ https://www.ncbi.nlm.nih.gov/pubmed/26574437 http://dx.doi.org/10.1021/ct501130r |
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