Escaping free-energy minima

By Alessandro Laio, Michele Parrinello. 2002

5,051 citations recorded by the source corpus.

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

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Citations in the corpus

Equivariant Flows: exact likelihood generative learning for symmetric densities (2020, methodology): “…to speed up rare events by adding a suitable bias energy to u(x) and subsequently correcting the generated distribution by reweighing or Monte-Carlo estimators using the ratio of true over generated density, e.g. (Torrie & Valleau, 1977; Bennett, 1976; Laio & Parrinello, 2002; Wu et al., 2016).”
Atomistic details of oxide surfaces and surface oxidation: the example of copper and its oxides (2015, background): “To this end, the combination of an accurate reactive potential with methods which allow for rare events to be probed, such as metadynamics [269] are possibly a way to go for this type of system.”
Protein storytelling through physics (2020, background): “Advances are coming from enhanced samplingmethods, such asmetadynamics (34), replica exchange molecular dynamics (REMD) (35), simulated annealing (36), adaptive force biasing (37), and umbrella sampling (38) [for reviews, see (39, 40), and for the basic concepts see (21, 41)].”
Equation-free: The computer-aided analysis of complex multiscale systems (2004, neutral): “…forms the basis of approaches, such as parallel replica MD (Voter, 1998), SWARM-MD (Huber and van Gunsteren, 1998), coarse extended Lagrangian dynamics (Iannuzzi et al., 2003; Laio and Parrinello, 2002), and simple averaging over multiple trajectories (Yeh and Hummer, 2002; Snow et al., 2002).”
Umbrella sampling (2011, background): “The aim of adaptive bias umbrella sampling 13 , 57–60 is to cover the whole range of interest of the reaction coordinate ξ in one simulation.”
Combining docking and molecular dynamic simulations in drug design (2006, methodology): “Parrinello and co-workers 183 employed a new MD method, metadynamics* 184 , to ﬁnd the correct conformation of ligands inside ﬂexible receptors in aqueous solution.”
Markov models of molecular kinetics: generation and validation. (2011, background): “generated by well-converged meta-dynamics [82] or replica-exchange [83] simulations), or more efficiently by launching trajectories from short local equilibrium dynamics restricted to the starting density μi(x) [84].”