In this study a 3 DoF mathematical model for the motions in surge, heave and pitch modes is utilized for investigating vertical accelerations of ships carrying WAP devices and while sailing in regular waves. Massive batches of simulated scenarios are carried out, in between which the wave length, wave steepness and ship heading are incrementally varied. Analysis of the results is performed within the scope of identifying vertical accelerations that may become severe. The hydrodynamics utilize the discretization of the hull geometry into flat triangular panels. Incident wave loads are calculated in real time as the simulation commences by accounting for the instantaneous wetted surface, while radiation and diffraction loads are pre-calculated and provided via appropriate interpolation tables and for the design waterline. The computations are performed for a research vessel hull and comparisons are made for the cases of standard propeller propulsion versus combined propeller and Flettner Rotor propulsion.