System includes a control system used to control operation of a vehicle system as the vehicle system moves along a route. The vehicle system includes a plurality of system vehicles in which adjacent system vehicles are operatively coupled such that the adjacent system vehicles are permitted to move relative to one another. The control system includes one or more processors that are configured to (a) receive operational settings of the vehicle system and (b) input the operational settings into a system model of the vehicle system to determine an observed metric of the vehicle system. The one or more processors are also configured to (c) compare the observed metric to a reference metric and (d) modify the operational settings of the vehicle system based on differences between the observed and the reference metrics.