The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics
Abstract
Metadynamics is a widely used and successful method for reconstructing the free‐energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well‐tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
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Cited by
Using metadynamics to explore complex free-energy landscapes
Bussi, G., & Laio, A. (2020) · Nature Reviews Physics · doi:10.1038/s42254-020-0153-0 · Cited by 718
Funnel metadynamics as accurate binding free-energy method
Limongelli, V., Bonomi, M., & Parrinello, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1303186110 · Cited by 411
Self-citationEnhanced sampling in molecular dynamics
Yang, Y. I., Shao, Q., Zhang, J., Yang, L., & Gao, Y. Q. (2019) · The Journal of Chemical Physics · doi:10.1063/1.5109531 · Cited by 398
TDP-43 α-helical structure tunes liquid–liquid phase separation and function
Conicella, A. E., Dignon, G. L., Zerze, G. H., Schmidt, H. B., D’Ordine, A. M., Kim, Y. C., Rohatgi, R., Ayala, Y. M., Mittal, J., & Fawzi, N. L. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912055117 · Cited by 375
Rethinking Metadynamics: From Bias Potentials to Probability Distributions
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Metadata
- Authors
- Bonomi, M., Barducci, A., & Parrinello, M.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2009-05-06
- Volume
- 30
- Issue
- 11
- Pages
- 1615-1621
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2028875836
- Cited by
- 354
- References
- 61
- FWCI
- 4.32
- Type
- journal article
- Language
- en
- Open access
- closed
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