Dear Sara,
Your understanding of how FAST and AeroDyn are linked is correct. AeroDyn will use information from FAST regarding the blade positions and velocities (not accelerations) to calculate the aerodynamic loads. So, as long as you specify proper blade positions and velocities, then the aerodynamic loads calculated by AeroDyn should be “correct.”
However, the problem with your approach is that it does not guarantee that the specified displacement, velocity, and acceleration of a DOF are consistent with the equations of motion, from which the loads output by FAST are calculated from. So, while the applied aerodynamic loads may be fine, the reaction loads output by FAST (including rotor thrust, RotThrust) – that are derived from a combination of applied and inertia loads – may not be correct. See the following forum topic for more information on FAST’s rotor thrust output: FAST Output: RotCt is not constant for the same TSR.
Best regards,