The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
A Time-Independent Free Energy Estimator for Metadynamics
Abstract
Metadynamics is a powerful and well-established enhanced sampling method for exploring and quantifying free energy surfaces of complex systems as a function of appropriately chosen variables. In the limit of long simulation time, metadynamics converges to the exact free energy surface plus a time-dependent constant. In this article, we analyze in detail this time-dependent constant. We show an easy way to calculate it, and by explicitly calculating the time dependence of this constant, we are able to derive a time-independent and locally convergent free energy estimator for metadynamics. We also derive an alternate procedure for obtaining the full unbiased distributions of generic operators from biased metadynamics simulations and explicitly test its usefulness.
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Cites
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
Self-citationT RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
Tiwary, P., & Parrinello, M. (2013) · Physical Review Letters · doi:10.1103/physrevlett.111.230602 · Cited by 494
Self-citationReaction coordinates of biomolecular isomerization
Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426
Cited by
Rethinking Metadynamics: From Bias Potentials to Probability Distributions
Invernizzi, M., & Parrinello, M. (2020) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.0c00497 · Cited by 359
Self-citationKinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
Tiwary, P., Limongelli, V., Salvalaglio, M., & Parrinello, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1424461112 · Cited by 347
Self-citationVariational Approach to Enhanced Sampling and Free Energy Calculations
Valsson, O., & Parrinello, M. (2014) · Physical Review Letters · doi:10.1103/physrevlett.113.090601 · Cited by 336
Self-citationMachine learning approaches for analyzing and enhancing molecular dynamics simulations
Wang, Y., Lamim Ribeiro, J. M., & Tiwary, P. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.12.016 · Cited by 303
Self-citationSpectral gap optimization of order parameters for sampling complex molecular systems
Tiwary, P., & Berne, B. J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600917113 · Cited by 259
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Metadata
- Authors
- Tiwary, P., & Parrinello, M.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-07-21
- Volume
- 119
- Issue
- 3
- Pages
- 736-742
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2314730640
- Cited by
- 514
- References
- 5
- FWCI
- 16.28
- Type
- journal article
- Language
- en
- Open access
- closed
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