  A general scheme, which includes constructions of coarse-grained (CG) models,
weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of
stable states, is presented to detect dynamical and thermodynamical properties
in complex systems. In the scheme, CG models are efficiently and accurately
optimized based on a directed distance from original to CG systems, which is
estimated from ensemble means of lots of independent observable in two systems.
Furthermore, WED independently generates multiple short molecular dynamics
trajectories in original systems. The initial conformations of the trajectories
are constructed from equilibrium conformations in CG models, and the weights of
the trajectories can be estimated from the trajectories themselves in
generating complete equilibrium samples in the original systems. CA calculates
the directed distances among the trajectories and groups their initial
conformations into some clusters, which correspond to stable states in the
original systems, so that transition dynamics can be detected without requiring
a priori knowledge of the states.
