MSM lag time cannot be used for variational model selection
Biomolecules
2019-11-26 v1 Biological Physics
Chemical Physics
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.
Cite
@article{arxiv.1708.08120,
title = {MSM lag time cannot be used for variational model selection},
author = {Brooke E. Husic and Vijay S. Pande},
journal= {arXiv preprint arXiv:1708.08120},
year = {2019}
}