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Escaping free-energy minima

Alessandro Laio, +1 more
- 01 Oct 2002 - 
- Vol. 99, Iss: 20, pp 12562-12566
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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.

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The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

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Towards a structural biology of the hydrophobic effect in protein folding

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References
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Journal ArticleDOI

Optimization by Simulated Annealing

TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
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Efficient, multiple-range random walk algorithm to calculate the density of states.

TL;DR: A new Monte Carlo algorithm is presented that permits us to directly access the free energy and entropy, is independent of temperature, and is efficient for the study of both 1st order and 2nd order phase transitions.
Journal ArticleDOI

Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events

TL;DR: In this article, a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids is derived, and the diffusion mechanism of a 10-atom Ag cluster on the Ag(111) surface using a $220\ensuremath{\mu}\mathrm{s}$ hyper-MD simulation.
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Constrained reaction coordinate dynamics for the simulation of rare events

TL;DR: In this article, a computationally efficient molecular dynamics method for estimating the rates of rare events that occur by activated processes is described, where the system is constrained at bottleneck regions on a general many-body reaction coordinate in order to generate a biased configurational distribution.
Journal ArticleDOI

Free energy from constrained molecular dynamics

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.
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