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Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
[Image: see text] Collective variable-based enhanced sampling methods are routinely used on systems with metastable states, where high free energy barriers impede the proper sampling of the free energy landscapes when using conventional molecular dynamics simulations. One such method is variationall...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9281396/ https://www.ncbi.nlm.nih.gov/pubmed/35762642 http://dx.doi.org/10.1021/acs.jctc.2c00197 |
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author | Pampel, Benjamin Valsson, Omar |
author_facet | Pampel, Benjamin Valsson, Omar |
author_sort | Pampel, Benjamin |
collection | PubMed |
description | [Image: see text] Collective variable-based enhanced sampling methods are routinely used on systems with metastable states, where high free energy barriers impede the proper sampling of the free energy landscapes when using conventional molecular dynamics simulations. One such method is variationally enhanced sampling (VES), which is based on a variational principle where a bias potential in the space of some chosen slow degrees of freedom, or collective variables, is constructed by minimizing a convex functional. In practice, the bias potential is taken as a linear expansion in some basis function set. So far, primarily basis functions delocalized in the collective variable space, like plane waves, Chebyshev, or Legendre polynomials, have been used. However, there has not been an extensive study of how the convergence behavior is affected by the choice of the basis functions. In particular, it remains an open question if localized basis functions might perform better. In this work, we implement, tune, and validate Daubechies wavelets as basis functions for VES. The wavelets construct orthogonal and localized bases that exhibit an attractive multiresolution property. We evaluate the performance of wavelet and other basis functions on various systems, going from model potentials to the calcium carbonate association process in water. We observe that wavelets exhibit excellent performance and much more robust convergence behavior than all other basis functions, as well as better performance than metadynamics. In particular, using wavelet bases yields far smaller fluctuations of the bias potential within individual runs and smaller differences between independent runs. Based on our overall results, we can recommend wavelets as basis functions for VES. |
format | Online Article Text |
id | pubmed-9281396 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-92813962022-07-15 Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials Pampel, Benjamin Valsson, Omar J Chem Theory Comput [Image: see text] Collective variable-based enhanced sampling methods are routinely used on systems with metastable states, where high free energy barriers impede the proper sampling of the free energy landscapes when using conventional molecular dynamics simulations. One such method is variationally enhanced sampling (VES), which is based on a variational principle where a bias potential in the space of some chosen slow degrees of freedom, or collective variables, is constructed by minimizing a convex functional. In practice, the bias potential is taken as a linear expansion in some basis function set. So far, primarily basis functions delocalized in the collective variable space, like plane waves, Chebyshev, or Legendre polynomials, have been used. However, there has not been an extensive study of how the convergence behavior is affected by the choice of the basis functions. In particular, it remains an open question if localized basis functions might perform better. In this work, we implement, tune, and validate Daubechies wavelets as basis functions for VES. The wavelets construct orthogonal and localized bases that exhibit an attractive multiresolution property. We evaluate the performance of wavelet and other basis functions on various systems, going from model potentials to the calcium carbonate association process in water. We observe that wavelets exhibit excellent performance and much more robust convergence behavior than all other basis functions, as well as better performance than metadynamics. In particular, using wavelet bases yields far smaller fluctuations of the bias potential within individual runs and smaller differences between independent runs. Based on our overall results, we can recommend wavelets as basis functions for VES. American Chemical Society 2022-06-28 2022-07-12 /pmc/articles/PMC9281396/ /pubmed/35762642 http://dx.doi.org/10.1021/acs.jctc.2c00197 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Pampel, Benjamin Valsson, Omar Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials |
title | Improving the Efficiency of Variationally Enhanced
Sampling with Wavelet-Based Bias Potentials |
title_full | Improving the Efficiency of Variationally Enhanced
Sampling with Wavelet-Based Bias Potentials |
title_fullStr | Improving the Efficiency of Variationally Enhanced
Sampling with Wavelet-Based Bias Potentials |
title_full_unstemmed | Improving the Efficiency of Variationally Enhanced
Sampling with Wavelet-Based Bias Potentials |
title_short | Improving the Efficiency of Variationally Enhanced
Sampling with Wavelet-Based Bias Potentials |
title_sort | improving the efficiency of variationally enhanced
sampling with wavelet-based bias potentials |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9281396/ https://www.ncbi.nlm.nih.gov/pubmed/35762642 http://dx.doi.org/10.1021/acs.jctc.2c00197 |
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