A method is disclosed for determining relative motion between equipment systems positioned on a structure that is subject to deformation due to vibrations, using accelerometers. Relative motion between equipment systems can introduce error into the targeting information provided to a system such as a weapons system, and thus the method facilitates compensation for such relative motion. A method is disclosed in which the raw accelerometer signals are filtered, then combined with attitude signals in a displacement calculation module (DCM). Within the DCM, the signals are manipulated to calculate, for each equipment system, the translational and rotational displacements due to hull modal vibration and the translational and rotational displacements due to force vibration. The sum of these values represent the movement of each of the affected equipment systems. Relative motion between systems is calculated as the difference between the calculated movement values.