dG=dH-TdS
so as T increases, so does the entropic contribution to the free
energy (=available energy). The potential energies stay the same when
using a temperature-independent forcefield (like all of the ones that
come with gromacs).
Your system will easily cross barriers on the order of KbT and thus
barriers are more easily crossed at higher temperature.
Nearly every RE paper has an introductory section that goes over these
topics in more or less detail. I suggest that you read the
introduction and theory sections of about 10 of them and you should by
then understand it very well.
Chris.
-- original message --
Hi,
Thank you for the reply. But in that case what helps the replica
at higher temperature cross the energy barrier? At higher temperature
the velocities will be higher.
Thanks in advance,
Sarbani
On Tue, 02 Dec 2008 Mark Abraham wrote :
[Hide Quoted Text]
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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