Coarse master equation from Bayesian analysis of replica molecular dynamics simulations

Saravanapriyan Sriraman, Yannis Kevrekidis, Gerhard Hummer

Research output: Contribution to journalArticle

101 Scopus citations

Abstract

We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.

Original languageEnglish (US)
Pages (from-to)6479-6484
Number of pages6
JournalJournal of Physical Chemistry B
Volume109
Issue number14
DOIs
StatePublished - Apr 14 2005

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry

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