[gmx-users] Questions regarding REMD simulation

michael zhenin mikelj25 at gmail.com
Sun Sep 18 13:35:43 CEST 2011

Hi All,

I have few questions regarding REMD simulation.

I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the simulation
(as described in Sugita and Okamoto publication, 1999). Then demux.pl and
trjcat collect the trajectories of the lowest temperature from each replica.

My problem is that while analyzing the results, I found in the edr
files that the temperatures along each replica are relatively

constant (+- 2K from the starting temperature) and the average temperature
is equal to the initial temperature.

How can this be explained? Does the temperature of each replica change
along the simulation or maybe the temperature of each

simulation stays close to its initial value and the coordinates are changed
between the different replica? (if so, why do i need to use

the post-processing tools such as the demux.pl script?)


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