up is exchanging with the next highest T, down is exchanging with the lower
T. These are attempted at alternate exchange attempts.
it looks like you have a problem near replica 5, you are not getting
exchanges and this effectively makes replica 4 your highest T.
check your temperature spacing and your potential energy overlap.
On Thu, Feb 23, 2023 at 6:16 AM Munazzah Fatima Ansari via AMBER <
amber.ambermd.org> wrote:
> Hello Developers,
> I am running the replica exchange molecular dynamics simulation for 12
> replicas. After the production run, it gave me a rem.log file. Now I am
> trying to find out the exchange acceptance ratio.
>
>
> To get the acceptance ratio, I use the following script:
>
>
> > cpptraj << EOF
> > readdata rem.log out crdidx 1,2,3,4,5,6,7,8,9,10,11,12
> > runanalysis remlog rem.log out trepidx.agr repidx name Tcrd acceptout
> > accept.dat
> > quit
> > EOF
>
> which gave me the trepidx.agr and accept.dat file
>
> Here I am unable to understand the output of accept.dat file which is
> given below:
>
>
> # DIMENSION 1
> #Replica %UP %DOWN
> 1 0.663 0.000
> 2 0.384 0.663
> 3 0.244 0.384
> 4 0.000 0.244
> 5 0.000 0.000
> 6 0.454 0.000
> 7 0.768 0.454
> 8 0.803 0.768
> 9 1.152 0.803
> 10 0.873 1.152
> 11 0.943 0.873
> 12 0.000 0.943
>
>
> What is the UP and DOWN show here ?
>
> Regards,
> Munazzah Fatima Ansari
>
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>
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Received on Thu Feb 23 2023 - 09:00:02 PST
