Free energy reconstruction from steered dynamics without post-processing

JOURNAL OF COMPUTATIONAL PHYSICS

卷:229

Article

Athenes, Manuel^1,2  Marinica, Mihai-Cosmin¹ 

[1] CEA Saclay, Serv Rech Met Phys, Dept Mat Nucl, F-91191 Gif Sur Yvette, France

[2] LLNL, Condensed Matter & Mat Div, Phys & Life Sci Directorate, Livermore, CA 94551 USA

关键词: Free-energy calculations;    Statistical thermodynamics;    Computer chemistry;    Molecular simulation;    Monte Carlo method;   

DOI  :  10.1016/j.jcp.2010.06.003

来源: Elsevier

【 摘 要 】

Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable one to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-a. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, we accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing. (C) 2010 Elsevier Inc. All rights reserved.

【 授权许可】

Free