An extensive investigation of influence of rub grooves on dynamics and stability of the rotor, which is subjected to aerodynamic forcing associated with the leakage flow through 44 straight-through seals, was performed by using numerical calculations based on the single control-volume method and the perturbation analysis. Three cases of different groove configurations were chosen for the comparative study, e.g., the seal without rub groove (case1), the seal with upstream shifting of the seal tooth in respect to the rub groove (case2) and the seal with location of the seal tooth in the middle station of the rub groove (case3). The orifice contract coefficient adopted in reduction of rotordynamic coefficients was provided by using Computational Fluid Dynamics (CFD). Influence of rub grooves on the leakage flow was obtained in terms of the close-up view of the flow pattern near the seal tooth, leakage flow rate, distributions of the mean pressure and circumferential velocity in cavities. In comparison to case 1, the leakage flow in case 3 is considerably intensified, while which in case 2 is slightly increased. Dynamics and instability of the rotor in all cases was discussed in terms of the rotordynamic coefficients and the logarithmic decrement, respectively. The results disclosed that the aerodynamic forcing in case 2 intensified the destabilization of the rotor system.