title: Obtaining fully dynamic coarse-grained models from MD.
abstract: We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected.
authors: Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141 E-28080, Madrid, Spain. pep@fisfun.uned.esc
authors: Pep
authors: P
authors: Español
authors: Ignacio
authors: I
authors: Zúñiga
mesh_terms: D001499:Bayes Theorem; D004058:Diffusion; D019277:Entropy; D056004:Molecular Dynamics Simulation