Computation of free energy profiles with parallel adaptive dynamics | Zendy

Tony Lelièvre | Zendy; Mathias Rousset | Zendy; Gabriel Stoltz | Zendy

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Computation of free energy profiles with parallel adaptive dynamics

Author(s) -

Tony Lelièvre,

Mathias Rousset,

Gabriel Stoltz

Publication year - 2007

Publication title -

the journal of chemical physics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.071

H-Index - 357

eISSN - 1089-7690

pISSN - 0021-9606

DOI - 10.1063/1.2711185

Subject(s) - metadynamics , computation , convergence (economics) , computer science , energy (signal processing) , non equilibrium thermodynamics , statistical physics , algorithm , theoretical computer science , computational science , molecular dynamics , mathematics , physics , statistics , quantum mechanics , economic growth , economics

4 pages, 1 FigureWe propose a formulation of adaptive computation of free energy differences, in the ABF or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows to present a truly unifying framework for these methods, and to prove convergence results for certain classes of algorithms. From a numerical viewpoint, a parallel implementation of these methods is very natural, the replicas interacting through the reconstructed free energy. We show how to improve this parallel implementation by resorting to some selection mechanism on the replicas. This is illustrated by computations on a model system of conformational changes

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