A method of controlling a linear motion system has a linear synchronous motor comprising a stator and at least two carrier units moveable in relation to the stator, the stator comprising a number of coil units, each of the at least two carrier units comprising a magnetic unit including an array of alternate-pole magnets having a regular magnet pole-pitch, wherein in order to form a train the at least two carrier units are arranged relative to each other so that the mutual distance between two identically poled magnets of two different magnetic units is an integer multiple of the magnet pole-pitch.