DOI: 10.3390/e16010163. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

10.3390/e16010163

Crossref journal-article

MDPI AG

Entropy (1968)

Abstract

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.

Bibliography

Abrams, C., & Bussi, G. (2013). Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. Entropy, 16(1), 163â199.

Authors 2

Cameron Abrams (first)
Giovanni Bussi (additional)

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Dates

Type	When
Created	11 years, 8 months ago (Dec. 27, 2013, 12:54 p.m.)
Deposited	1 year, 3 months ago (May 31, 2024, 8:51 p.m.)
Indexed	1 week, 5 days ago (Aug. 26, 2025, 2:26 a.m.)
Issued	11 years, 8 months ago (Dec. 27, 2013)
Published	11 years, 8 months ago (Dec. 27, 2013)
Published Online	11 years, 8 months ago (Dec. 27, 2013)

Funders 0

None

BibTeX

@article{Abrams_2013, title={Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration}, volume={16}, ISSN={1099-4300}, url={http://dx.doi.org/10.3390/e16010163}, DOI={10.3390/e16010163}, number={1}, journal={Entropy}, publisher={MDPI AG}, author={Abrams, Cameron and Bussi, Giovanni}, year={2013}, month=dec, pages={163–199} }

JSON

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  "abstract": "<jats:p>We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.</jats:p>",
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  "page": "163-199",
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  "title": "Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration",
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