[AMBER] Query regarding Acceptance ratio file

From: Munazzah Fatima Ansari via AMBER <amber.ambermd.org>
Date: Thu, 23 Feb 2023 16:46:08 +0530

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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Received on Thu Feb 23 2023 - 03:30:03 PST
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