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Enhanced sampling without borders: on global biasing functions and how to reweight them

Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of biomolecular motions in atomistic resolution. However, the high computational demand of these simulations limits the timescales of motions that can be observed. To resolve this issue, so called enhanced sampling...

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Detalles Bibliográficos
Autores principales: Kamenik, Anna S., Linker, Stephanie M., Riniker, Sereina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society of Chemistry 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8768491/
https://www.ncbi.nlm.nih.gov/pubmed/34935813
http://dx.doi.org/10.1039/d1cp04809k
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author Kamenik, Anna S.
Linker, Stephanie M.
Riniker, Sereina
author_facet Kamenik, Anna S.
Linker, Stephanie M.
Riniker, Sereina
author_sort Kamenik, Anna S.
collection PubMed
description Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of biomolecular motions in atomistic resolution. However, the high computational demand of these simulations limits the timescales of motions that can be observed. To resolve this issue, so called enhanced sampling techniques are developed, which extend conventional MD algorithms to speed up the simulation process. Here, we focus on techniques that apply global biasing functions. We provide a broad overview of established enhanced sampling methods and promising new advances. As the ultimate goal is to retrieve unbiased information from biased ensembles, we also discuss benefits and limitations of common reweighting schemes. In addition to concisely summarizing critical assumptions and implications, we highlight the general application opportunities as well as uncertainties of global enhanced sampling.
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spelling pubmed-87684912022-02-15 Enhanced sampling without borders: on global biasing functions and how to reweight them Kamenik, Anna S. Linker, Stephanie M. Riniker, Sereina Phys Chem Chem Phys Chemistry Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of biomolecular motions in atomistic resolution. However, the high computational demand of these simulations limits the timescales of motions that can be observed. To resolve this issue, so called enhanced sampling techniques are developed, which extend conventional MD algorithms to speed up the simulation process. Here, we focus on techniques that apply global biasing functions. We provide a broad overview of established enhanced sampling methods and promising new advances. As the ultimate goal is to retrieve unbiased information from biased ensembles, we also discuss benefits and limitations of common reweighting schemes. In addition to concisely summarizing critical assumptions and implications, we highlight the general application opportunities as well as uncertainties of global enhanced sampling. The Royal Society of Chemistry 2021-12-14 /pmc/articles/PMC8768491/ /pubmed/34935813 http://dx.doi.org/10.1039/d1cp04809k Text en This journal is © the Owner Societies https://creativecommons.org/licenses/by/3.0/
spellingShingle Chemistry
Kamenik, Anna S.
Linker, Stephanie M.
Riniker, Sereina
Enhanced sampling without borders: on global biasing functions and how to reweight them
title Enhanced sampling without borders: on global biasing functions and how to reweight them
title_full Enhanced sampling without borders: on global biasing functions and how to reweight them
title_fullStr Enhanced sampling without borders: on global biasing functions and how to reweight them
title_full_unstemmed Enhanced sampling without borders: on global biasing functions and how to reweight them
title_short Enhanced sampling without borders: on global biasing functions and how to reweight them
title_sort enhanced sampling without borders: on global biasing functions and how to reweight them
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8768491/
https://www.ncbi.nlm.nih.gov/pubmed/34935813
http://dx.doi.org/10.1039/d1cp04809k
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