Autocorellation function - how is compute existance of hbond

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GROMACS version: 2018.4
GROMACS modification: No
I have a question. I want to know one thing. How is computing autocorrelation function, because I am not sure about something.

I try to calculate the autocorrelation function by myself. This is what I get when I calculate the autocorrelation function for water bridges.

wykres
wykres3508×2479 198 KB

I calculate in that way.

  1. I made a list of all hydrogen bonds for every frame, but I modified data to have a list of hydrogen bonds, as not atom number, but molecule number like
    MGD229 SOL16475
    MGD229 SOL114
    MGD230 SOL10760
    MGD230 SOL7563
    MGD230 SOL5056
    MGD233 SOL8573
    MGD233 SOL11772
    MGD234 SOL8331

  2. Then I compare a list of hydrogen bonds from every frame always to the first frame and I print to output these hydrogen bonds which are present in both frames (present and first).

  3. Then I calculate water bridges. So for example in the first frame, I have 480 water bridges, so I calculate that: 480/480 = 1, then in the third frame I have 240 water bridges, so I have 240/480 = 0,5, then in the 1000th frame 120, so 120/480 = 0,25.

And now there is a time for a question. If I havefor example hydrogen bonds like
MGD100 SOL1000
and I have this hydrogen bond in the first frame and in the second frame, but then in the third, fourth, fifth, sixth, seventh, eighth, ninth frame I don’t have this hydrogen bond, but then in the tenth frame this hydrogen bond appears again, so should I count this hydrogen bonds or not (it was not existing for an 8 ps). On the one hand, it is both in the first frame and tenth frame, but on the other hand, it was not existing for 8 ps (1 frame in my case is 1 ps).

I found gmx hbond file, but I can’t find my answer
https://raw.githubusercontent.com/gromacs/gromacs/master/src/gromacs/gmxana/gmx_hbond.cpp

Or maybe you know, who was programming gmx hbond program, because when I write in my terminal gmx hbond I have a big list of persons and I don’t know, which person I should contact

                  :-) GROMACS - gmx hbond, 2018.4 (-:

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