  We describe a systematic approach to construct coarse-grained Markov state
models from molecular dynamics data of systems driven into a non-equilibrium
steady state. We apply this method to study the globule-stretch transition of a
single tethered model polymer in shear flow. The folding/unfolding rates of the
coarse-grained model agree with the original detailed model. We demonstrate
that the folding/unfolding proceeds through the same narrow region of
configuration space but along different cycles.
