From a theoretical point of view, translation and rotation should not be projected out of the partial Hessian because, while some normal modes resemble translation and rotation, they are, in fact, collective vibrations between the QM and MM subsystems. We refer to those modes as pseudo-translation and pseudo-rotation. Instead of projecting out translation and rotation from the partial Hessian, a more effective approach is to identify modes with pseudotranslational and pseudo-rotational contributions that exceed a threshold and remove them since they are not well described.