Vibrational spectroscopy is widely used to gain insights into structural and dynamic properties of chemical, biological and material systems. Thus, an efficient and accurate method to simulate vibrational spectra is desired. In this paper, we justify and employ a microcanonical molecular simulation scheme to calculate the vibrational spectra of three challenging water clusters: the neutral water dimer (H 4 O 2 ), the protonated water trimer (H 7 O + 3 ), and the protonated water tetramer (H 9 O + 4 ). We find that with the accurate description of quantum nuclear delocalization effects through the constrained nuclear-electronic orbital framework, including vibrational mode coupling effects through molecular dynamics simulations can additionally improve the vibrational spectrum calculations. In contrast, without the quantum nuclear delocalization picture, 1