Another option of TrapApp is to rescale ion velocities for a fixed
temperature. This algorithm is quite simple--- after each finite difference
propagation, the temperature of the ions
is calculated and the velocities of the ions are rescaled by the
square-root of the ratios of the ion temperature to the desired temperature:
Although this algorithm may initially appear physically unjustified,
its effect is simply to keep the ions at constant temperature. Thus, the
temperature-scaling option is analogous to achieving
constant temperature by placing the configuration in thermal contact with a
large reservoir.