Metadynamics

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]

  1. ^ 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.
  2. ^ 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.
  3. ^ 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.
  4. ^ 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.
  5. ^ Cite error: The named reference welltuned was invoked but never defined (see the help page).
  6. ^ 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.
  7. ^ 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