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 journalArticle

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

Fingerprint

Free energy
free energy
Statistics
statistics
Kinetics
kinetics
cells
Byproducts
Trajectories
trajectories
simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials. / Maragliano, Luca; Vanden Eijnden, Eric; Roux, Benoît.

In: Journal of Chemical Theory and Computation, Vol. 5, No. 10, 10.2009, p. 2589-2594.

Research output: Contribution to journalArticle

@article{b3a6c1bc630b43fd96514c337454ba84,
title = "Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials",
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.",
author = "Luca Maragliano and {Vanden Eijnden}, Eric and Beno{\^i}t Roux",
year = "2009",
month = "10",
doi = "10.1021/ct900279z",
language = "English (US)",
volume = "5",
pages = "2589--2594",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",
number = "10",

}

TY - JOUR

T1 - Free energy and kinetics of conformational transitions from voronoi tessellated milestoning with restraining potentials

AU - Maragliano, Luca

AU - Vanden Eijnden, Eric

AU - Roux, Benoît

PY - 2009/10

Y1 - 2009/10

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=73949127824&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=73949127824&partnerID=8YFLogxK

U2 - 10.1021/ct900279z

DO - 10.1021/ct900279z

M3 - Article

AN - SCOPUS:73949127824

VL - 5

SP - 2589

EP - 2594

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 10

ER -