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

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


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.