[gmx-users] replica exchange

rob yang nextgame at hotmail.com
Tue Nov 1 22:58:58 CET 2005

1 more quick q:
mpirun -np 2  mdrun_mpi -s input.tpr -np 2 -replex 1000
do I need a -multi flag here? i've seen people using -multi flag but I can 
get it to run without it so what gives?

thank you


>From: Xavier Periole <x.periole at rug.nl>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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>Subject: Re: [gmx-users] replica exchange
>Date: Tue, 01 Nov 2005 17:20:11 +0100
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>rob yang wrote:
>>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.
>first case.
>>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?
>That is your choice !! Depend on what your are interested in !! And mixing 
>temperatures is not generally
>what is interesting. One advantages of REMD is to generate properties over 
>a range of temperatures...
>>thank you very much in advance.
>Xavier Periole - Ph.D.
>Dept. of Biophysical Chemistry / MD Group   Univ. of Groningen
>Nijenborgh 4
>9747 AG Groningen
>The Netherlands
>Tel: +31-503634329
>Fax: +31-503634800
>email: x.periole at rug.nl
>web-page: http://md.chem.rug.nl/~periole
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