In the paper simulation of the indentation of iron crystal was carried out using the method of molecular dynamics. We investigated the effect of vibrations on the AE under the impact of a single element (indenter) with a certain amount of material. Fluctuations of the forces acting on the sensor, changing of the system energy and the formation of defects during loading were analyzed. The force signal showed the increase in its amplitude and power spectrum as well as the median frequency drop under loading by vibrating indenter. The rationale behind all these changes may be dependence between the vibration amplitude and full system energy