[gmx-users] replica exchange output information
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 7 19:22:30 CET 2008
David Mobley wrote:
> 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?
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.
> 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
> 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.
While we're at the topic of REMD, I'd like to make a shameless plug for
our new website that predicts appropriate temperatures for REMD
simulations. Check out http://folding.bmc.uu.se/remd
> David Mobley
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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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