We study the vibrational properties of the protonated water dimer and its deuterated forms at room temperature. Molecular dynamics simulations within the empirical valence bond (EVB) model are used to generate the vibrational spectra that are interpreted using the effective modes analysis (EMA). Quantum effects are taken into account through an effective parametrization of the EVB model. EMA allows for the assignment of the bands in the 1000 - 2000 cm-1 region of the protonated water dimer from the molecular dynamics trajectory. It is then found that although this system is very anharmonic the two main bands in this spectral region arise from a linear coupling between the asymmetric OH+O stretch and asymmetric bend of the two water molecules. This mixing explains the simulated band shifts upon isotopic substitution of the central proton or of the hydrogens of the two water molecules. © 2011 American Institute of Physics.