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

Brooke E Husic; Vijay S Pande

doi:10.1063/1.5002086

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.

Authors

Brooke E Husic¹, Vijay S Pande¹

Affiliation

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.

Grants and funding

R01 GM062868/GM/NIGMS NIH HHS/United States