A method for use in controlling a free piston Stirling machine having a cold end and a warm end and driven by a linear motor having an armature winding to which a drive voltage is applied. The method comprises (a) sensing internal mechanical collisions; (b) repeatedly sensing the temperature of the cold end, the temperature of the warm end and the drive voltage; (c) storing, as associated data, a value representing drive voltage, the temperature of the cold end and the temperature of the warm end at the time of sensed collisions; and (d) limiting the drive voltage to less than the drive voltage that was sensed at a collision and is stored in association with stored warm end and cold end temperatures that are proximate currently sensed warm end and cold end temperatures.