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Title: Nonparametric variational optimization of reaction coordinates

State of the art realistic simulations of complex atomic processes commonly produce trajectories of large size, making the development of automated analysis tools very important. A popular approach aimed at extracting dynamical information consists of projecting these trajectories into optimally selected reaction coordinates or collective variables. For equilibrium dynamics between any two boundary states, the committor function also known as the folding probability in protein folding studies is often considered as the optimal coordinate. To determine it, one selects a functional form with many parameters and trains it on the trajectories using various criteria. A major problem with such an approach is that a poor initial choice of the functional form may lead to sub-optimal results. Here, we describe an approach which allows one to optimize the reaction coordinate without selecting its functional form and thus avoiding this source of error.
Authors:
;  [1]
  1. Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT (United Kingdom)
Publication Date:
OSTI Identifier:
22493212
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 18; Other Information: (c) 2015 Author(s); Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; CHEMICAL REACTIONS; COMPUTERIZED SIMULATION; COORDINATES; EQUILIBRIUM; ERRORS; OPTIMIZATION; PROTEINS; TRAJECTORIES; VARIATIONAL METHODS