Is there a downside to using the “large-amplitude nonlinear model for w.f. loads” in very deep water where the amplitudes of vessel motion are always negligible compared to the water depth?
Yes, the “large-amplitude” nonlinear model can become problematic in very deep water. It is best to turn this option off unless alerted by the simulation that the water depth may be too shallow for the linearized model. Still, it never hurts to run both, if possible, and see if any quantities of interest to you change significantly.
