The article deals with a simulation approach to the representation of the ship motions in waves, interacting with the propulsion system behavior (diesel engine and propeller). The final goal is the development of a simulator, as complete as possible, that allows the analysis of the main engine thermodynamics in different sea conditions, also in the unfavorable event of dynamic instability of the hull, and the correct management of the other propulsion components. This latter aspect is particularly interesting in some of the last new energy solutions for decarbonization of ships, concerning, for example, auxiliary electric motors, powered by batteries, to support the traditional diesel-mechanical propulsion (especially in heavy weather conditions). From this point of view, a proper analysis of the engine dynamic performance, affected by particular sea states, is fundamental for a smart management and control of shaft generators/auxiliary electric motors, batteries, etc. To this end, the work presents and highlights the main features of a ship simulator, suitable for the study of the new propulsion solutions that are emerging in maritime transport. Some representative results will point out the complex non-linear behavior of the propulsion plant in waves. Moreover, a parametric roll scenario will be investigated, in order to highlight the capability of the conceived simulator in modeling the effects of the dynamic instability of the hull on the propulsion plant.