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

Note: MSM Lag Time Cannot Be Used for Variational Model Selection

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Free PMC article

Note: MSM Lag Time Cannot Be Used for Variational Model Selection

Brooke E Husic et al. J Chem Phys. .
Free PMC article

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.

Figures

FIG. 1.
FIG. 1.
The flow chart shows several ways to create a MSM from raw simulation data. The blue box indicates which of the parameters enumerated can be optimized using the GMRQ. The MSM lag time and number of timescales scored must be held constant. This figure is adapted with permission from Husic et al., J. Chem. Phys. 145, 194103 (2016). Copyright 2016 AIP Publishing LLC.

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