Hi, I have run a REMD, which including 46 replicas. I searched how to analyze my REMD statistics, but I am still confused how to analyze my result; how to generate a continuous a energy distribution curve; how to deal with 46 .log files. It seems so complicated.
one of my md.log file is as below: Replica exchange at step 998000 time 1996.00000 Repl 18 <-> 19 dE_term = 1.690e+01 (kT) Repl ex 0 1 2 3 4 x 5 6 x 7 8 x 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl pr .01 .17 .03 1.0 1.0 .00 .00 .01 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 Replica exchange statistics Repl 499 attempts, 250 odd, 249 even Repl average probabilities: Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl .07 .08 .05 .05 .06 .06 .06 .06 .06 .05 .05 .04 .03 .05 .03 .03 .03 .01 .03 .02 .04 .02 .02 .02 .01 .02 .02 .01 .01 .01 .01 .01 .01 .01 .01 .02 .01 .01 .02 .00 .02 .00 .02 .02 .01 Repl number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl 14 20 13 12 16 14 15 17 14 15 9 12 8 13 7 5 7 2 5 6 10 6 4 6 2 5 3 1 6 3 3 3 2 3 4 5 2 3 4 2 4 2 4 4 3 Repl average number of exchanges: Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl .06 .08 .05 .05 .06 .06 .06 .07 .06 .06 .04 .05 .03 .05 .03 .02 .03 .01 .02 .02 .04 .02 .02 .02 .01 .02 .01 .00 .02 .01 .01 .01 .01 .01 .02 .02 .01 .01 .02 .01 .02 .01 .02 .02 .01 I wonder whether the result is ideal, do I need to optimize my temperature distribution. Best regards ouyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
