[gmx-users] replica exchange output information
Mark.Abraham at anu.edu.au
Tue Jan 8 00:00:38 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).
For the record, I found the output sufficiently clear to write my own
perl scripts for collecting exchange statistics.
>>> 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 is documented in the manual - section 3.13
More information about the gromacs.org_gmx-users