Dear Emma
For the calculation of the Wannier centres the localisation of the molecular orbitals has to be performed on the optimised electronic structure.
Hence for each configuration for which the WC are needed, also the MOS are needed, the trajectory is not enough.
If it is enough to have the WC every N MD time step, one possibility would be to run REFTRAJ on the generated trajectory, with a stride N, where for each selected configuration a new wave function optimization is performed. Choosing this option you can select the settings also differently from what was used in MD.
Though for the IR spectrum it is recommended to compute the dipole quite frequently to resolve properly the high frequencies.
Kind regards
Marcella