Markov state models based on milestoning

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

Research output: Contribution to journalArticlepeer-review


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
Issue number20
StatePublished - May 28 2011

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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