[gmx-users] replica exchange

rob yang nextgame at hotmail.com
Tue Nov 1 16:55:30 CET 2005

Hi gmxers,
I have a general question about the implementation behind RE in 3.3.  if I 
were to run the following command:
mpirun -np 2  mdrun_mpi -s input.tpr -np 2 -replex 1000

where there are 2 .tpr files already made in the directory: input0.tpr, 
and I have defined 2 independent computers linked by network.

would gromacs run the two sim independently on the two computers and only 
communicate with each other every 1000 steps? or
would gromacs try to run 1 sim parallelly on both computers first and then 
the other? ie: constant communication between the 2 computers through 
network which would definately be slower.

In case the above command makes no sense, here's what I want to do:
given two sims differred only by the temperature, I'd like to run RE using 
two boxes with the swapping rate being every 1000 steps. Ideally, I'd like 
to have one sim per box, which only talks to each other at the swapping 

p.s.  another q on how to analyze the results.  Should I concat input0.trr 
and input1.trr into a single file at the end of the run? Or treat them as 
two separate and independent runs?

thank you very much in advance.


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