The Stochastic Difference Equation as a Tool to Compute Long Time Dynamics

Abstract

Molecular Dynamics (MD) simulations provide an atomically detailed description of complex systems on a wide range of temporal and spatial scales. Despite numerous successes and many insightful observations, a clear limitation of the MD approach is its short time scales. Routine simulations of complex and large molecular systems at the atomically level of detail are restricted to nanoseconds. This time scale is far too short to address many interesting processes in biophysics, such as conformational transitions, transport phenomena and reactions.