[gmx-users] Hydrogen bond autocorrelation

Gmx QA gmxquestions at gmail.com
Tue Jun 18 15:58:47 CEST 2019

Dear list,

This has been discussed many times previously on the list, but I still have
some questions about hydrogen bond autocorrelation functions.

I have run a simulation with single molecule of a compound in water which
can form exactly one inter-molecular hydrogen bond. From the hbnum.xvg
time-series (i.e. the existence function) of this h-bond I then have a
python-script to calculate the acf. The script seems to work because the
resulting acf-function looks exactly the same as the corresponding function
computed with xmgrace. But it is very different from what I get from gmx
hbond -ac.

I read a lot about continuous vs intermittent acfs for h-bonds, the latter
being called non-continuous in the van der Spoel et al. 2006-paper I think.
Is the reason for the discrepancy simply that gmx hbond -ac calculates a
_different_ acf than you get from the hbnum.xvg file (and xmgrace)?

Then, going forward, after I compute the acf and in the most basic case fit
to y = a* exp(-t/b), does the value of b correspond to the life-time of the
h-bond? Or it is the integral (from 0 to inf) that gives you the lifetime?
This seems to be treated differently by different people.

Thanks a bunch

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