[gmx-users] exchanged pairs in the log file of a remd simulation
David van der Spoel
spoel at xray.bmc.uu.se
Sun Feb 3 10:46:28 CET 2008
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.
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
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