MSM lag time cannot be used for variational model selection

Published 27 Aug 2017 in q-bio.BM, physics.bio-ph, and physics.chem-ph | (1708.08120v1)

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 lag time of the operator being approximated must be held constant in the variational approach.

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