  Extracting the kinetic properties of a system whose dynamics depend on the pH
of the environment with which it exchanges energy and atoms requires sampling
the Grand Canonical Ensemble. As an alternative, we present a novel strategy
that requires simulating only the most recurrent Canonical Ensembles that
compose the Grand Canonical Ensemble. The simulations are used to estimate the
Gran Canonical distribution for a specific pH value by reweighting and to
construct the transition rate matrix by discretizing the Fokker-Planck equation
by Square Root Approximation and robust Perron Cluster Cluster Analysis. As an
application, we have studied the tripeptide Ala-Asp-Ala.
