Determination of reaction coordinates via locally scaled diffusion map

Mary A. Rohrdanz, Wenwei Zheng, Mauro Maggioni, Cecilia Clementi

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161 Scopus citations

Abstract

We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available.

Original languageEnglish (US)
Article number124116
JournalJournal of Chemical Physics
Volume134
Issue number12
DOIs
StatePublished - Mar 28 2011

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ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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