Fluorescence is commonly exploited to probe microscopic properties. An important example is tryptophan in protein environments, where variations in fluorescence quantum yield, and in absorption and emission maxima, are used as indicators of changes in the environment. Modeling the fluorescence quantum yield requires the determination of both radiative and non-radiative decay constants, both on the potential energy surface of the excited fluorophore. Furthermore, the inclusion of complex environments implies their accurate representation as well as extensive configurational sampling. In this work, we present and test various methodologies based on TD-DFT and QM-MM molecular dynamics that take all these requirements into account to provide a ...