Molecular dynamics simulation of complex systems can be speeded up by tricks on full-scale atomic dynamics. or by drastically reducing the number of degrees of freedom. In the realm of tricks one can incorporate constraints for hard degrees of freedom, reconstruct particles from a reduced description, or change the masses of particles with the aim to reduce the bandwidth of motional modes. For proteins in water the time step can be increased more than tenfold by these tricks.
Really slow events can be described on an appropriate reaction coordinate. In the limit of high friction and a single reaction coordinate, the flux can be described analytically (in the Smoluchowski limit) with steady state solutions of the stochastic flux equations. The potential of mean force and the diffusion constant must be known, but these can be obtained from atomic simulations at intermediate points, with constraints on the reaction coordinate.
The permeation of small molecules through a bilayer membrane and the slow process of substrate transport into the active site of a protein, are examples where this approach works well.