Dear Diwas Bajracharya

While performing nonlinear response history analysis, the seismic input is defined by ground accelerations applied at the base nodes. The acceleration of the masses lumped at each floor is called the response acceleration which can be obtained only after performing the analysis.

Rohan

The ground motions should be applied on the soil foundation of the building in the numerical model analysis.

But for hand-doing, you should consider to apply them to masses of your system.