[gmx-users] REMD problem in concept

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 3 16:56:59 CET 2008


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.


-- original message --

      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 :

[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.


More information about the gromacs.org_gmx-users mailing list