Enhanced sampling in the well-tempered ensemble
- PMID: 20866953
- DOI: 10.1103/PhysRevLett.104.190601
Enhanced sampling in the well-tempered ensemble
Abstract
We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi, J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Gō model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.
Similar articles
-
Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble.J Chem Theory Comput. 2012 Jul 10;8(7):2189-92. doi: 10.1021/ct300297t. Epub 2012 Jun 20. J Chem Theory Comput. 2012. PMID: 26588950
-
Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages.J Chem Theory Comput. 2012 Oct 9;8(10):3777-92. doi: 10.1021/ct300061g. Epub 2012 Apr 23. J Chem Theory Comput. 2012. PMID: 26593019
-
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
-
Enhanced sampling algorithms.Methods Mol Biol. 2013;924:153-95. doi: 10.1007/978-1-62703-017-5_7. Methods Mol Biol. 2013. PMID: 23034749 Review.
-
Generalized-ensemble algorithms for molecular simulations of biopolymers.Biopolymers. 2001;60(2):96-123. doi: 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F. Biopolymers. 2001. PMID: 11455545 Review.
Cited by
-
The Parkinson disease-linked LRRK2 protein mutation I2020T stabilizes an active state conformation leading to increased kinase activity.J Biol Chem. 2014 May 9;289(19):13042-53. doi: 10.1074/jbc.M113.537811. Epub 2014 Apr 2. J Biol Chem. 2014. PMID: 24695735 Free PMC article.
-
Mapping transiently formed and sparsely populated conformations on a complex energy landscape.Elife. 2016 Aug 23;5:e17505. doi: 10.7554/eLife.17505. Elife. 2016. PMID: 27552057 Free PMC article.
-
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.PLoS One. 2015 Jun 8;10(6):e0125941. doi: 10.1371/journal.pone.0125941. eCollection 2015. PLoS One. 2015. PMID: 26053419 Free PMC article.
-
Ab initio mechanism revealing for tricalcium silicate dissolution.Nat Commun. 2022 Mar 10;13(1):1253. doi: 10.1038/s41467-022-28932-2. Nat Commun. 2022. PMID: 35273192 Free PMC article.
-
Multiple routes and milestones in the folding of HIV-1 protease monomer.PLoS One. 2010 Oct 13;5(10):e13208. doi: 10.1371/journal.pone.0013208. PLoS One. 2010. PMID: 20967249 Free PMC article.
LinkOut - more resources
Full Text Sources
