[gmx-users] exchanged pairs in the log file of a remd simulation
OZENGIN at KU.EDU.TR
Sun Feb 3 17:38:01 CET 2008
Thank you for your answers! You are right, Mark. I looked at the md1.log file and when I looked at the others I saw that there were different pairs other than 1-2 and 2-3.
Consequently, there is no problem then. All the pairs, providing their energies are overlapped sufficiently, are exchanged? Is it what is happening?
From: "Mark Abraham" <mark.abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Sun, 3 Feb 2008 20:50:55 +1100 (EST)
Subject: Re: [gmx-users] exchanged pairs in the log file of a remd simulation
> Hi all,
> I am performing replica exchange MD simulations. Here, I attach the part
> of a log file which gives info about the exchanges made at step 46000 and
> 47000. It is just a test run. As you can see, on the line 2, it is
> indicated that the exchange is made between the rep 1 and rep 2 or between
> the repl2 and repl3. The case is the same for other time steps.
> There are no other types of pairs.
> Replica exchange at step 46000 time 92
> Line 2: Repl 1 <-> 2 dE = 3.006e-01
> Repl ex 0 1 x 2 3 x 4 5 x 6 7 x 8 9 x 10 11 x 12
> Repl pr .74 1.0 1.0 .70 .40 1.0
> Replica exchange at step 47000 time 94
> Line 2: Repl 2 <-> 3 dE = 7.473e-01
> Repl ex 0 x 1 2 3 4 x 5 6 x 7 8 x 9 10 11 12
> Repl pr .04 .47 1.0 1.0 .65 .60 .34
I'd guess that you're looking at your *_1.log and thus you're seeing the
numbers for the successful exchanges for only this replica. In the GROMACS
implementation, I guess that the potential energies are only swapped
between current exchange pairs, and not distributed to the whole replica
system. Thus different .log files will probably have different such lines,
because only two of the replicas have the necessary information.
Odd and even pairs are considered for exchange at alternate exchange
attempts, of course, as described in the manual. The 'x' characters denote
succesful exchanges, as you will see documented early on in the log file
(e.g. grep "^Repl " *.log)
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