[gmx-users] replica exchange output information

[David Mobley]

All,

Probably this should be obvious, but I've looked over the manual and
the wiki and the information is eluding me: When running replica
exchange in gromacs, are the output files written by replica number,
or by temperature number? That is, does ener0.edr, traj0.trr, etc.,
contain information for the simulation running at the temperature
specified in topol0.tpr, or does it contain information for the
replica initiated as #0 (and initially at the temperature in
topol0.tpr) which may then change temperatures as swaps happen?

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.

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?

Thanks!
David Mobley
UCSF
http://www.dillgroup.ucsf.edu/~dmobley