Effect of molecular vibrations on the absorption spectra simulated via a sequential approach combining molecular dynamics (MD) with quantum-chemical calculations has been investigated. Simulated spectra have been obtained from the time-dependent density functional theory results averaged over series of molecular geometries retrieved from Born–Oppenheimer MD trajectories. Distributions of bond lengths have been analyzed and related to the features of calculated spectra. For NVE simulations of small systems, absorption spectra exhibit bimodal bandshape as a result of classical treatment of vibrations. For NVE trajectories of larger systems or simulations in the NVT ensemble calculated absorption bands are symmetric, however, they may not agree with the results of Franck–Condon analysis. These results are practical manifestations of effects predicted theoretically from general principles. Consequences for the modeling of absorption spectra have been discussed. © 2013 Wiley Periodicals, Inc.