  The time sequences of the molecular dynamics simulation for the folding
process of a protein is analyzed with the inherent structure landscape which
focuses on configurational dynamics of the system. Time dependent energy and
entropy for inherent structures are introduced and from these quantities a
conformational temperature is defined. The conformational temperature follows
the time evolution of a slow relaxation process and reaches the bath
temperature when the system is equilibrated. We show that the nonequilibrium
system is described by two temperatures, one for fast vibration and the other
for slow configurational relaxation, while the equilibrium system is by one
temperature. The proposed formalism is applicable widely for the systems with
many metastable states.
