[gmx-users] replica exchange output information
dmobley at gmail.com
Mon Jan 7 19:40:44 CET 2008
> The order is that from low temperature to high temperature (as you could
> check from the edr files) and when swaps happen the coordinates and
> boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by temperature.
> > As a follow-up question, is there an easy way (i.e. some output file
> > written) to track which replica number is at a particular temperature
> > (equivalently, a log of swaps between replicas)? I'd like to be able
> > to monitor mixing between my replicas.
> Yes, check src/contrib/scripts/demux.pl
OK. It would still be nice to have documented what goes into the log
file in sufficient detail that I could use the info myself (i.e. to
write a python code that would do something similar).
> > I had thought this information would be written to some sort of output
> > file, but I'm not seeing anything special aside from the occasional
> > info in the log file which looks something like this:
> > Replica exchange at step 9500 time 19
> > Repl 14 <-> 15 dE = 1.572e+00 dpV = 1.544e-04 d = 1.572e+00
> > Repl ex 0 x 1 2 x 3 4 5 6 x 7 8 9 10 11 12
> > x 13 14 15
> > Repl pr 1.0 .22 .41 .55 .20 .27
> > .13 .21
> > I can't find where it's explained what this information means. For
> > example, why are there x's between some numbers and not others?
> x means exchanges, demux.pl makes sense of it, but you need to make sure
> that you save your md0.log file.
x means successful exchanges? And am I reading the log right that
exchanges are attempted between alternating pairs of replicas, i.e.
the 0->1 exchange is attempted one time, and then the 1->2 exchange
the next time?
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