Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

By Alessandro Laio, Francesco Luigi Gervasio. 2008

1,456 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/d2e70a35b896bc9a46f3d9625f27e361a700e2bb

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In Atomic and Molecular Physics, and Optics

In Statistical and Nonlinear Physics

Citations in the corpus

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “The bias is used to keep the memory of the already explored zones of the phase space, and to discourage the system to visit them again (Laio and Gervasio, 2008).”
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation (2014, methodology): “8 Importantly, aMD does not require any prede ﬁ ned reaction coordinate(s), unlike other biased free energy calculation methods, including the umbrella sampling, 9 metadynamics, 10 adaptive biasing force (ABF) calculations, 11 and orthogonal space sampling.”
Molecular dynamics simulation for all (2018, positive): “…MD; Schlitter et al., 1994), pushing a simulation away from regions of conformational space it has already visited (e.g., metadynamics; Laio and Gervasio, 2008), raising the effective temperature associated with certain degrees of freedom (e.g., replica exchange and temperatureaccelerated MD;…”
Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design (2013, methodology): “Metadynamics is another technique designed to accelerate rare events and reconstruct the free energy proﬁle (47).”
Molecular dynamics simulations and novel drug discovery (2018, neutral): “umbrella sampling [88], and metadynamics [89].”
Effect of moisture on the mechanical properties of CFRP–wood composite: An experimental and atomistic investigation (2015, methodology): “During the simulation using the metadynamics approach [55], the free energy profiles of the cellulose–epoxy interface are constructed and plotted in Fig.”
Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, methodology): “The locality of the mean forces motivates a separation of the N-body PMF A(RN) ∗In principle, it is possible to measure the value of the PMF directly, for example, using Metadynamics.”