Trajectory calculations stochastic differential equation

Recently Calderon introduced a surrogate process approximation (SPA) to improve the sampling in calculation of the JE. The scheme is applied to the study of the unravelling of deca-alanine at constant temperature in a steered molecular dynamics simulation. The distribution of the work is approximated by developing a model for the dynamics using a relatively small number of real trajectories in conjunction with stochastic differential equations selected to model the process. The... 

At its most basic level, molecular dynamics is about mapping out complicated point sets using trajectories of a system of ordinary differential equations (or, in Chaps. 6-8, a stochastic-differential equation system). The sets are typically defined as the collection of probable states for a certain system. In the case of Hamiltonian dynamics, they are directly associated to a region of the energy landscape. The trajectories are the means by which we efficiently explore the energy surface. In this chapter we address the design of numerical methods to calculate trajectories. 

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