[gmx-users] Questions regarding REMD simulation

[gal.fradin at live.biu.ac.il]

Dear Michael,
First  I want to say thank you very much... for posting you questions here.
I can't help you with this but I wish you Good Luck and that you will find your answers soon!
Best wishes,thanks again,
Gal :)

Date: Sun, 18 Sep 2011 14:35:43 +0300
From: mikelj25 at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Questions regarding REMD simulation



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?)

Thanks,

Michael






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