sarbani chattopadhyay wrote:
Hi everybody,
I am having a doubt whether I have understood the
concepts of Replica
exchange molecular dynamics correctly or not.
When a pair of replicas are exchanged, the one at
higher temperature thet has
higher velocities, (which are rescaled after the exchange) comes with a
higher energy. It's
kinetic energy gets reduced as velocities are rescaled. Thus its
potential energy increases.
Kinetic energy is a function of the velocities, potential energy is a
function of the positions. So velocity rescaling will not have any
instantaneous effect on the PE.
What happens to the replica that was at lower temperature? It's
velocities need to be increased
to maintain the temperature. What happens to it's potential energy then?
As before, nothing.
I may be missing a very basic point and any suggestion regarding this
will be highly helpful.
Once the simulation continues, things are still normal. The reason the
exchange occurred was that the positions were such that the PE was close
enough that detailed balance for the generalized ensemble was preserved
during the swap. Thus the ensembles before and after the exchange are
also still well-formed.
Mark
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