[gmx-users] Replica exchange probabilities beyond version 2016
Pritam Ganguly
pganguly at chem.ucsb.edu
Tue Apr 14 02:00:41 CEST 2020
Hello,
I have noticed that the average exchange probability for a replica
exchange run increases significantly if I use Gromacs versions 2018, as
compared to versions 2016 or earlier. I have tested that by simulating
the same system with versions 2016.4 and 2018.3 and the average
probabilities I find are:
Version 2016.4:
Replica exchange statistics
Repl 1666 attempts, 833 odd, 833 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 46 47 48 49 50 51 52 53 54 55 56 57
58 59 60 61 62 63
Repl .29 .33 .29 .30 .28 .30 .30 .29 .29 .29 .30 .26
.29 .30 .28 .29 .26 .26 .29 .28 .26 .27 .27 .27 .27 .28
.26 .27 .26 .25 .27 .25 .26 .27 .25 .24 .25 .26 .27 .25
.27 .26 .26 .26 .25 .26 .26 .24 .25 .27 .26 .27 .26 .25
.27 .27 .28 .26 .27 .26 .27 .27 .28
Version 2018.3:
Replica exchange statistics
Repl 1666 attempts, 833 odd, 833 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 46 47 48 49 50 51 52 53 54 55 56 57
58 59 60 61 62 63
Repl .39 .39 .37 .42 .38 .38 .39 .36 .36 .38 .40 .39
.40 .39 .37 .35 .40 .39 .35 .38 .40 .35 .38 .35 .36 .35
.36 .36 .38 .36 .37 .36 .35 .36 .36 .37 .35 .35 .35 .37
.37 .35 .37 .36 .37 .34 .36 .38 .38 .38 .35 .37 .36 .39
.36 .40 .38 .38 .40 .36 .37 .36 .33
These are test runs for 5 ns with exchange frequencies of 3 ps. I have
used the same input parameters for both of these runs (mdp is attached).
I actually observed this with many other systems and I was looking for
any relevant gromacs release note for versions 2018 or beyond related to
the replica exchange algorithm or the way the energies are calculated,
but I could not figure it out.
Regards,
Pritam
--
Pritam Ganguly
Department of Chemistry and Biochemistry
University of California at Santa Barbara
Santa Barbara, CA, USA 93106
Office: PSBN 3606
Phone: +1-805-893-2767
http://people.chem.ucsb.edu/ganguly/pritam
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