Nano-indentation of silicon is analyzed using the molecular dynamics simulation with an initial configuration deformed by the elastic solution in order to diminish the computational time. Comparing the usual procedures with the perfectly undeformed initial configuration, almost similar internal structural change of occurrence of amorphous-phase and emission of a dislocation loop are observed. From the crystallographic analyses to determine a Bergers vector, a dislocation loop is found to be formed by combining the 60 degree dislocation with the screw dislocation.