Markov state models based on milestoning

Christof Schtte, Frank Noé, Jianfeng Lu, Marco Sarich, Eric Vanden Eijnden

Research output: Contribution to journalArticle

Abstract

Markov state models (MSMs) have become the tool of choice to analyze large amounts of molecular dynamics data by approximating them as a Markov jump process between suitably predefined states. Here we investigate "Core Set MSMs", a new type of MSMs that build on metastable core sets acting as milestones for tracing the rare event kinetics. We present a thorough analysis of Core Set MSMs based on the existing milestoning framework, Bayesian estimation methods and Transition Path Theory (TPT). We show that Core Set MSMs can be used to extract phenomenological rate constants between the metastable sets of the system and to approximate the evolution of certain key observables. The performance of Core Set MSMs in comparison to standard MSMs is analyzed and illustrated on a toy example and in the context of the torsion angle dynamics of alanine dipeptide.

Original languageEnglish (US)
Article number204105
JournalJournal of Chemical Physics
Volume134
Issue number20
DOIs
StatePublished - May 28 2011

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Markov processes
Dipeptides
alanine
tracing
Alanine
Torsional stress
torsion
Molecular dynamics
Rate constants
molecular dynamics
Kinetics
kinetics

ASJC Scopus subject areas

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

Cite this

Markov state models based on milestoning. / Schtte, Christof; Noé, Frank; Lu, Jianfeng; Sarich, Marco; Vanden Eijnden, Eric.

In: Journal of Chemical Physics, Vol. 134, No. 20, 204105, 28.05.2011.

Research output: Contribution to journalArticle

Schtte, Christof ; Noé, Frank ; Lu, Jianfeng ; Sarich, Marco ; Vanden Eijnden, Eric. / Markov state models based on milestoning. In: Journal of Chemical Physics. 2011 ; Vol. 134, No. 20.
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