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.