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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
