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A generalized parallel replica dynamics

Andrew J. Binder 1 Tony Lelièvre 2, 3 Gideon Simpson 4 
CERMICS - Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique, Inria Paris-Rocquencourt, ENPC - École des Ponts ParisTech
Abstract : Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming-Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation on the algorithm is illustrated on various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.
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Submitted on : Friday, April 25, 2014 - 9:31:55 AM
Last modification on : Friday, November 18, 2022 - 9:24:00 AM

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Andrew J. Binder, Tony Lelièvre, Gideon Simpson. A generalized parallel replica dynamics. Journal of Computational Physics, 2015, 284, ⟨10.1016/⟩. ⟨hal-00983282⟩



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