[gmx-users] REMD problem in concept
sarbani_c84 at rediffmail.com
Tue Dec 2 19:01:29 CET 2008
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,
On Tue, 02 Dec 2008 Mark Abraham wrote :
>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.
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