[gmx-users] replica exchange output information
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 7 19:55:37 CET 2008
David Mobley wrote:
>> 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).
More info is usually better, however demux.pl md0.log should get you
going. Meanwhile, as you probably are aware, we are considering some
other REMD varieties, and that will probably mean we will need to add
>>> 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?
That's correct. Formally you need to consider all possible pairs of
replicas, but if you take them far enough apart then the possibility of
a i-i+2 exchange is negligible.
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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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