Molecular dynamics at low time resolution

The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step Delta t used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than Delta t, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps Delta t. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein. (C) 2010 American Institute of Physics. [doi:10.1063/1.3493459]