A granular system composed of frictional glass beads is simulated using the discrete element method. The intergrain forces are based on the Hertz contact law in the normal direction with frictional tangential force. The damping due to collision is also accounted for. Systems are loaded at various stresses and their quasistatic elastic moduli are characterized. Each system is subjected to an extensive dynamic testing protocol by measuring the resonant response to a broad range of ac drive amplitudes and frequencies via a set of diagnostic strains. The system, linear at small ac drive amplitudes, has resonance frequencies that shift downward (i.e., modulus softening) with increased ac drive amplitude. Detailed testing shows that the slipping contact ratio does not contribute significantly to this dynamic modulus softening, but the coordination number is strongly correlated to this reduction. This suggests that the softening arises from the extended structural change via break and remake of contacts during the rearrangement of bead positions driven by the ac amplitude.