Exchange probability exchange values

User discussions
1

how can I make sure that those values of replica are good … for example, those for step 1000 and step 2000

Replica exchange at step 1000 time 2.00000
Repl ex  0    1    2    3    4    5    6    7    8    9   10   11 x 12   13   14   15   16   17   18   19   20   21 x 22   23   24   25   26   27 x 28   29 x 30   31   32   33   34   35
Repl pr        .02       .02       .04       .07       .06       1.0       .10       .04       .01       .19       1.0       .05       .47       1.0       .31       .35       .32     

Replica exchange at step 2000 time 4.00000
Repl ex  0    1    2    3 x  4    5    6    7 x  8    9   10   11   12   13   14   15 x 16   17   18   19 x 20   21   22   23 x 24   25 x 26   27   28   29 x 30   31 x 32   33 x 34   35
Repl pr        .06       .11       .02       1.0       .14       .03       .09       1.0       .14       .68       .62       .25       1.0       .13       .03       1.0       1.0
2

Exchange probabilities vary over time because different conformations are sampled. You values look ok to me.

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3

appreciate your reply , excuse me I wait until the simulation finished and got this results but i couldn’t sure that are those results are good or not as I used the temperatures from Temperature generator for REMD-simulations

Replica exchange statistics
Repl 96798 attempts, 48399 odd, 48399 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
Repl .34 .35 .36 .37 .37 .38 .39 .39 .39 .41 .41 .41 .42 .43 .43 .44 .44 .45 .45 .46 .47 .47 .47 .48 .48 .49 .49 .50 .50 .51 .51 .52 .52 .52 .59
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
Repl 16475 17098 17239 17642 17945 18188 18721 18804 19048 19454 19769 20052 20408 20610 20892 21119 21524 21586 21674 22333 22623 22858 23096 23055 23507 23634 23754 24029 24319 24671 24749 25069 24927 25440 28749
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
Repl .34 .35 .36 .36 .37 .38 .39 .39 .39 .40 .41 .41 .42 .43 .43 .44 .44 .45 .45 .46 .47 .47 .48 .48 .49 .49 .49 .50 .50 .51 .51 .52 .52 .53 .59

4

Those probabilities are very high. You can use much fewer replicas.

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6

thanks a lot but how can i select the suitable range of temperatures to have a good probability value? is there a specific condition or equation to do that or just I need to reduce the numbers? Appreciate your help

7

There is an online tool, but the site is down. Here is the reference:
A temperature predictor for parallel tempering simulations - Physical Chemistry Chemical Physics (RSC Publishing)!

I would think that in your case you can simply use half the number of replicas.