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To average over a thermodynamic quantity it suffices to average over the
values for the sequence of states generated by the Metropolis algorithm.
However it is usually wise to carry out a number of Monte-Carlo steps
before starting to do any averaging. This is to guarantee that the
system is in thermodynamic equilibrium while the averaging is carried
out.
The sequence of random changes is often considered as a sort of time
axis. In practice we think (e.g. ) about the time required to reach
equilibrium. Sometimes, however, the transition rate becomes very low and
the system effectively gets stuck in a non-equilibrium state. This is
often the case at low temperatures when almost every change causes an
increase in energy.