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This article presents a time dependent density functional theory (TDDFT) implementation to prop-agate the Kohn-Sham equations in real time, including the effects of a molecular environmentthrough a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers anall-electron description employing Gaussian basis functions, and incorporates the Amber force-fieldin the QM-MM treatment. The most expensive parts of the computation, comprising the commutatorsbetween the hamiltonian and the density matrix?required to propagate the electron dynamics?, andthe evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run ongraphics processing units, which remarkably accelerates the performance of the code. The methodwas validated by reproducing linear-response TDDFT results for the absorption spectra of severalmolecular species. Two different schemes were tested to propagate the quantum dynamics: (i) aleap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches wereconfronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules.Interestingly, the presence of iron was found to seriously limitate the length of the integration timestep, due to the high frequencies associated with the core-electrons. This highlights the importanceof pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nucleiare present. Finally, the methodology was applied to investigate the shifts induced by the chemicalenvironment on the most intense UV absorption bands of two model systems of general relevance:the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In bothcases, shifts of several nanometers are observed, consistently with the available experimental data.