[gmx-users] exchanged pairs in the log file of a remd simulation

[David van der Spoel]

OZGE ENGIN wrote:
> 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. 
> 
> Why?
> 
Other exchanges are not attempted, although this is not entirely 
correct. However since the probability for exchanges is ver small when 
the energy overlap is small this is not a serious approximation. In your 
case it seem like you have quite high probabilities however, indicating 
that your temperature spacing is quite small. In that case exchanges 1-3 
could be possible, but these are not attempted in gromacs.


> 
> 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   13
> 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   13
> Repl pr   .04       .47       1.0       1.0       .65       .60       .34
> 
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se