Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling

B. Fačkovec, Eric Vanden Eijnden, D. J. Wales

Research output: Contribution to journalArticle

Abstract

A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

Original languageEnglish (US)
Article number044119
JournalJournal of Chemical Physics
Volume143
Issue number4
DOIs
StatePublished - Jul 28 2015

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Relaxation time
sampling
Sampling
Markov processes
cells
Molecular dynamics
relaxation time
Computer simulation
estimators
positioning
partitions
molecular dynamics
matrices
simulation

ASJC Scopus subject areas

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

Cite this

Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling. / Fačkovec, B.; Vanden Eijnden, Eric; Wales, D. J.

In: Journal of Chemical Physics, Vol. 143, No. 4, 044119, 28.07.2015.

Research output: Contribution to journalArticle

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