Phytochromes are red/far-red light-sensing photoreceptor proteins that undergo reversible structural changes when absorbing light. Upon photon absorption, structural changes in the bilin chromophore (an open-chain tetrapyrrole) propagate initially to its binding pocket and subsequently throughout the entire protein, ultimately triggering biological function. This chapter presents a comprehensive multiscale strategy for tracking the entire sequence of events, beginning with the initial electronic excitation in the embedded chromophore up to the large-scale structural changes in the protein. The approach integrates nonadiabatic quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations with fully classical (MM) MD and enhanced sampling techniques. All key steps are provided in a practical, implementation-focused format: from system setup, force-field parametrization, and excited-state simulations, to long-time classical simulations that explore global protein conformational changes. While our examples focus on bacteriophytochromes, the computational pipeline described here can be adapted to any photoactive protein to elucidate its light-driven reaction coordinates.