In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton-phonon coupling computed from a Born-Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects. K E Y W O R D S absorption lineshape, spectral density, QM/MM molecular dynamics 1 | INTRODUCTIONThe accurate modeling of electronic absorption spectra is a fundamental tool to understand and complement experimental data. Experimental and computational techniques are widely used to identify molecular species and to predict environment effects on the molecular response and photochemistry.From a computational point of view, many different approaches have been exploited in theoretical spectroscopy. [1][2][3][4] The most basic one applied to the simulation of absorption spectra, is based on the computation of the excitation energies of a dye in the ground-state equilibrium geometry, including, if necessary, the solvent effects with an implicit model 5-8 or within an atomistic approach. 9-16 These vertical excitation energies are then compared to the maxima of the corresponding experimental absorption bands. This approach is commonly used, even to benchmark the level of theory for excited-state simulations against experiments. 17 However, comparison of vertical excitation energies can easily become inadequate when accurate estimations of the absorption spectrum are needed. 1 The coupling of electronic transitions to nuclear degrees of freedom (DOFs), for example, generates a characteristic vibronic progression, and can result in an asymmetrical lineshape even when the vibronic structure is hidden in homogeneous and inhomogeneous broadening. 18 Other factors, such as the configurations sampled by the chromophore and the finite lifetime of the excited state, contribute to the spectral shape.For molecules in condensed phase, peaks positions and intensities in the absorption spectra are also affected by the interactions with the inhomogeneous environment, owing to the many different configurations that the solvent adopts around the molecule. The resulting spectra are thus broadened by the many possible solvatochromic shifts.A method able to reproduce both peak positions and line shapes would be of crucial importance to the computatio...