The charged beam moving in the accelerator is modelled by particle-in-cell method. The control with delay in the connection canal is simulated by the aftereffect. Thus, the model is described by system of the differential equations with delay. We observe and estimate changes of particles coordinates in the cross-section of the accelerator. It is supposed that initial conditions are the set with random error and we have chance of updating the solution in periodic timepoints with the same error. The dependence between the estimate dispersion and the measuring error dispersion is recieved.