Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Alessandro Laio and Michele Parrinello in 2002[1] and is usually applied within molecular dynamics simulations. MTD closely resembles a number of newer methods such as adaptively biased molecular dynamics,[2] adaptive reaction coordinate forces[3] and local elevation umbrella sampling.[4] More recently, both the original and well-tempered metadynamics[5] were derived in the context of importance sampling and shown to be a special case of the adaptive biasing potential setting.[6] MTD is related to the Wang–Landau sampling.[7]
^Laio, A.; Parrinello, M. (2002). "Escaping free-energy minima". Proceedings of the National Academy of Sciences of the United States of America. 99 (20): 12562–12566. arXiv:cond-mat/0208352. Bibcode:2002PNAS...9912562L. doi:10.1073/pnas.202427399. PMC 130499. PMID 12271136.
^Babin, V.; Roland, C.; Sagui, C. (2008). "Stabilization of resonance states by an asymptotic Coulomb potential". J. Chem. Phys. 128 (2): 134101/1–134101/7. Bibcode:2008JChPh.128b4101A. doi:10.1063/1.2821102. PMID 18205437.
^Barnett, C.B.; Naidoo, K.J. (2009). "Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): An application to ring puckering". Mol. Phys. 107 (8): 1243–1250. Bibcode:2009MolPh.107.1243B. doi:10.1080/00268970902852608. S2CID 97930008.
^Hansen, H.S.; Hünenberger, P.H. (2010). "Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water". J. Comput. Chem. 31 (1): 1–23. doi:10.1002/jcc.21253. PMID 19412904. S2CID 7367058.
^Cite error: The named reference welltuned was invoked but never defined (see the help page).
^Dickson, B.M. (2011). "Approaching a parameter-free metadynamics". Phys. Rev. E. 84 (3): 037701–037703. arXiv:1106.4994. Bibcode:2011PhRvE..84c7701D. doi:10.1103/PhysRevE.84.037701. PMID 22060542. S2CID 42243972.
^Christoph Junghans, Danny Perez, and Thomas Vogel. "Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang–Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics." Journal of Chemical Theory and Computation 10.5 (2014): 1843-1847. doi:10.1021/ct500077d
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device, a type of device file in Linux for interacting with flash memory Metadynamics, a computer simulation method in computational physics, chemistry and...
techniques such as accelerated-MD simulations, replica exchange simulations, metadynamics, multicanonical MD simulations, or methods using coarse-grained representation...
the folding of proteins. The Wang–Landau sampling is related to the metadynamics algorithm. The Wang and Landau algorithm is used to obtain an estimate...
potential (as done in the metadynamics method) or the bias potential can be used for umbrella sampling (as done in metadynamics with umbrella sampling corrections...
the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation". Journal of the American Chemical Society. 132 (24): 8291–8300...
including density functional theory (DFT), molecular dynamics, docking, and metadynamics. The distribution coefficient predictions were introduced for the first...
stresses have to be high. Some authors have used the term 'postdynamic' or 'metadynamic' to describe recrystallization that occurs during the cooling phase of...
Effect of Antagonist Vismodegib on Smoothened Receptor Deactivation Using Metadynamics Simulation". Front Chem. 7: 406. Bibcode:2019FrCh....7..406Y. doi:10...
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