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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2021
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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. |
format | Online Article Text |
id | pubmed-8768491 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
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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