In this study, the seismic response of a building equipped with an MR damper is examined through RTHS testing. This work aims to prove the robustness of an adaptive model-based compensation (AMBC) algorithm with adaptive gain calibration in non-linear specimens such as MR dampers. For this purpose, a benchmark problem is studied in a virtual environment using Matlab/Simulink, with an MR damper as the experimental substructure controlled by a clipped optimal control algorithm with Linear Quadratic Gaussian (LQG). The results show that AMBC provides robustness to RTHS tests against synchronization errors and uncertainty due to highly non-linear specimens with time-dependent properties.