Periodic vortex shedding behind a circular cylinder is investigated by the DSMC method with an improved new collision scheme. The new collision scheme (U-system 3) that can deal with large cell dimensions conserves the total energy of each collision pair precisely during an intermolecular collision and the stability of the scheme improves furthermore. The lock-in phenomena in which a frequency of vortex production is synchronized with the frequency of the cylinder vibration are confirmed in the DSMC calculation.