Escaping free-energy minima
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TLDR
A powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates is introduced.Abstract:
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.read more
Citations
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Molecular Docking: Shifting Paradigms in Drug Discovery.
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String method in collective variables: Minimum free energy paths and isocommittor surfaces
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Neural network potential-energy surfaces in chemistry: a tool for large-scale simulations
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Combining docking and molecular dynamic simulations in drug design.
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Constructing high-dimensional neural network potentials: A tutorial review
TL;DR: In this paper, the basic ideas of neural network potentials are presented with a special focus on developing NNPs for high-dimensional condensed systems, and a recipe for the construction of these potentials is given and remaining limitations of the method are discussed.
References
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Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
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Constrained reaction coordinate dynamics for the simulation of rare events
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Free energy from constrained molecular dynamics
Michiel Sprik,Giovanni Ciccotti +1 more
TL;DR: In this article, the blue-moon ensemble method was used to compute the potential of mean force and transmission coefficient of a given reaction coordinate in the case of an arbitrary reaction coordinate.