  Based on multiple parallel short molecular dynamics simulation trajectories,
we designed the reweighted ensemble dynamics (RED) method to more efficiently
sample complex (biopolymer) systems, and to explore their hierarchical
metastable states. Here we further present an improvement to depress
statistical errors of the RED and we discuss a few keys in practical
application of the RED, provides schemes on selection of basis functions,
determination of free parameter in the RED. We illustrate the application of
the improvements in two toy models and in the solvated alanine dipeptide. The
results show the RED enable to capture the topology of multiple-state
transition networks, to detect the diffusion-like dynamical behavior in
entropy-dominated system, and to identify solvent effects in the solvated
peptides. The illustrations serve as general applications of the RED in more
complex biopolymer systems.
