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

Efficient Estimation of Transition Rates as Functions of pH