GROMACS version: 2018.4

GROMACS modification: No

I have some questions. I want to compute average hbond lifetime between lipids and water molecules. To do this I use ACF http://manual.gromacs.org/documentation/2020-beta1/reference-manual/analysis/hydrogen-bonds.html

For example gmx hbond -f eq3_900_1000.xtc -s eq3.tpr -b 900000 -e 950000 -ac eq3_ac.xvg

- I get time (0-5000 ps) and 4 values, but I can’t find good description. In my xvg file I have

@ s0 legend “Ac\sfin sys\v{}\z{}(t)”

@ s1 legend “Ac(t)”

@ s2 legend “Cc\scontact,hb\v{}\z{}(t)”

@ s3 legend “-dAc\sfs\v{}\z{}/dt”

This is my images (x - time from 0 to 5000 ps, and 4 different values)

2.Why in the first value (“Ac\sfin sys\v{}\z{}(t)”) at the end I have negative number like -0.0175003

The first two values are autocorrelation function, but third and fourth?

Gromacs use this to calculate the autocorrelation function

3. But which of my value 1. “Ac\sfin sys\v{}\z{}(t)” or 2. “Ac(t)” is this properly autocorrelation function?

When I have a function, how to compute hydrogen bond lifetime. I see that I can do this using this from instruction “with si(t)={0,1} for H-bond i at time t. The integral of C(τ) gives a rough estimate of the average H-bond lifetime τHB:” http://manual.gromacs.org/documentation/2020-beta1/reference-manual/analysis/hydrogen-bonds.html

So first I should try obtain function form (but exponential will be e^x?) and then I definite integral from 0 to 5000 (my time is from 0 to 5000 ps)???

I read also something like that

“In general, these decays involve different simultaneous

processes, and hence the corresponding plots can be fitted to a

sum of exponentials”

where T i is the time constant and Ai the amplitude of the ith

individual decay process and N is the number of exponentials.

N is generally not known beforehand. Because of the nonorthogonality of the exponentials, unambiguous determination of the

proper values for Ti , Ai , and N is not easy."

- So how to calculate A and T?

Thanks in advance