[gmx-users] replica exchange output information

[David Mobley]

David,

> 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?

Thanks,
David