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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
