A dynamic simulation method suppressing uninteresting degrees of freedom

In order to be able to simulate slow or infrequent motions which require extremely long (or sometimes impossibly long) simulations, a method of simulation using an equation of motion with the uninteresting degrees of freedom suppressed—the generalized Langevin equation—has been used. This method obtains the memory function and effective potential used in the generalized Langevin equation by fitting to the fast motion behavior of a full simulation with all of the degrees of freedom retained. Hence, only a relatively short time full simulation is necessary. The method was tested on two model problems: a two-dimensional potential model designed to mimic conformational transitions and a two-dimensional array of ellipsoids (representing benzene rings) interacting with nearest-neighbor potentials. In both cases, the results obtained simulating with a reduced number of degrees of freedom are in good agreement with the results of the full simulation.