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J Chem Phys. 2017 Nov 7;147(17):176101. doi: 10.1063/1.5002086.

Note: MSM lag time cannot be used for variational model selection.

Author information

1
Department of Chemistry, Stanford University, Stanford, California 94305, USA.

Abstract

The variational principle for conformational dynamics has enabled the systematic construction of Markov state models through the optimization of hyperparameters by approximating the transfer operator. In this note, we discuss why the lag time of the operator being approximated must be held constant in the variational approach.

PMID:
29117698
PMCID:
PMC5669980
[Available on 2018-11-07]
DOI:
10.1063/1.5002086

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