[gmx-users] Replica exchange probabilities and extend simulation

[Christian Blau]

Hi Ahmed,


If you have a look into "Optimal temperature ladders in replica exchange simulations", available here:

https://www.sciencedirect.com/science/article/pii/S000926140900356X

you will see that your exchange probabilities should be a bit higher. Then again, you might have to set up a lot more 
simulations, which you can get around with more advanced protocols like solute tempering (REST). These methods are 
implemented in PLUMED for example.


If you want further insight, I suggest using

demux.pl md.log

It's a good sign if you see single replicas walking through the whole temperature range, it's a bad sign if you see that 
some replicas only stay close to a certain temperature.


Best,

Christian


On 2020-01-09 14:58, hind ahmed wrote:
> Dear All,
>
>   Are these probabilities good? and how can I extend the simulation of replica-exchange?
>
> Thanks
>
> Replica exchange statistics
> Repl  14999 attempts, 7500 odd, 7499 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
> Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02
> 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
> Repl      259  263  270  330   62   57   63   58   65   67   71   74   89   87   88  103  100  103   98   98  114   93  132  127  149  111  117  126  129  124  145
> 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
> Repl      .03  .04  .04  .04  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .01  .02  .01  .02  .02  .02  .01  .02  .02  .02  .02  .02
>