  We show how accurate kinetic information, such as the rates of protein
folding and unfolding, can be extracted from replica-exchange molecular
dynamics (REMD) simulations. From the brief and continuous trajectory segments
between replica exchanges, we estimate short-time propagators in conformation
space and use them to construct a master equation. For a helical peptide in
explicit water, we determine the rates of transitions both locally between
microscopic conformational states and globally for folding and unfolding. We
show that accurate rates in the ~1/(100 ns) to ~1/(1 ns) range can be obtained
from REMD with exchange times of 5 ps, in excellent agreement with results from
long equilibrium molecular dynamics.
