Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials

Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux

Research output: Contribution to journalLetter

Abstract

Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the "milestones", placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this "Voronoi tessellated milestoning" method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.

Original languageEnglish (US)
Pages (from-to)2589-2594
Number of pages6
JournalJournal of chemical theory and computation
Volume5
Issue number10
DOIs
StatePublished - Oct 2009

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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