doi: 10.1103/PhysRevLett.100.020603.
Epub 2008 Jan 18.
Well-tempered metadynamics: a smoothly converging and tunable free-energy method
Affiliations
- PMID: 18232845
- DOI: 10.1103/PhysRevLett.100.020603
Item in Clipboard
Well-tempered metadynamics: a smoothly converging and tunable free-energy method
Phys Rev Lett.
.
Abstract
We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.
Similar articles
-
Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation.J Chem Theory Comput. 2014 Sep 9;10(9):3626-33. doi: 10.1021/ct500441q. J Chem Theory Comput. 2014. PMID: 26588507
-
Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations.J Chem Theory Comput. 2014 Aug 12;10(8):2975-86. doi: 10.1021/ct500012b. J Chem Theory Comput. 2014. PMID: 26588271
-
Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms.Acc Chem Res. 2015 Feb 17;48(2):277-85. doi: 10.1021/ar500356n. Epub 2014 Dec 12. Acc Chem Res. 2015. PMID: 25496113 Review.
-
Path finding on high-dimensional free energy landscapes.Phys Rev Lett. 2012 Jul 13;109(2):020601. doi: 10.1103/PhysRevLett.109.020601. Epub 2012 Jul 9. Phys Rev Lett. 2012. PMID: 23030145
-
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.J Comput Chem. 2009 Aug;30(11):1615-21. doi: 10.1002/jcc.21305. J Comput Chem. 2009. PMID: 19421997
Cited by
-
Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels.Nat Commun. 2024 May 31;15(1):4628. doi: 10.1038/s41467-024-48823-y. Nat Commun. 2024. PMID: 38821927 Free PMC article.
-
A reactive neural network framework for water-loaded acidic zeolites.Nat Commun. 2024 May 17;15(1):4215. doi: 10.1038/s41467-024-48609-2. Nat Commun. 2024. PMID: 38760371 Free PMC article.
-
Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package.J Phys Chem B. 2024 May 23;128(20):4959-4974. doi: 10.1021/acs.jpcb.4c01987. Epub 2024 May 14. J Phys Chem B. 2024. PMID: 38742764
-
Effective data-driven collective variables for free energy calculations from metadynamics of paths.PNAS Nexus. 2024 Apr 12;3(4):pgae159. doi: 10.1093/pnasnexus/pgae159. eCollection 2024 Apr. PNAS Nexus. 2024. PMID: 38665160 Free PMC article.
-
Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.J Chem Theory Comput. 2024 May 14;20(9):3492-3502. doi: 10.1021/acs.jctc.4c00223. Epub 2024 Apr 25. J Chem Theory Comput. 2024. PMID: 38662196 Free PMC article.
LinkOut - more resources
Full Text Sources
Other Literature Sources
