A shake table test is conducted for the three-story reinforced concrete building structure using 0.28 g, 0.5 g, 0.75 g, and 1.0 g of seismic input motions based on the Gyeongju earthquake. Computational efforts are made in parallel to explore the mechanical details in the structure. For engineering practice, the elastic modulus of concrete and rebar in the dynamic analysis is reduced to 38% and 50%, respectively, to calibrate the structure's natural frequencies. The engineering approach to the reduced modulus of elasticity is believed to be due to the inability to specify the flexibility of the actual boundary conditions. This aspect may lead to disadvantages of nonlinear dynamic analysis that can distort local stress and strain relationships. The initial elastic modulus can be applied directly without the so-called engineering adjustment with infinite element models with spring and spring-dashpot boundary conditions. This has the advantage of imposing the system flexibility of the structure on the sub-boundary conditions of springs and damping devices to control its sensitivity in a serial arrangement. This can reflect the flexibility of realistic boundary conditions and the effects of system damping (such as the gap between a concrete footing and shake table, loosening of steel anchors, etc.) in scalar quantities. However, these spring and dashpot coefficients can only be coordinated based on experimental results, making it challenging to select the coefficients in-prior to perform an experimental test.