[gmx-users] Hydrogen bond autocorrelation

Gmx QA gmxquestions at gmail.com
Wed Jun 19 09:40:30 CEST 2019

Hi David

Thanks for your email. In this case, I explicitly select only the compound
itself when computing hydrogen bonds, so while I see your point about
water-mediated h-bonds, the results (including the act-function) are the
same regardless of -nomerge.

Could you comment on whether the h-bond computed in gromacs corresponds to
the continuous or the intermittent definition of a h-bond? I think the
latter, but I am not sure. And are there any consequences later that would
depend on which h-bond acf is used, such as for example when fitting an
exponential function for determining the life time of the (single) bond?


Den ons 19 juni 2019 kl 08:26 skrev David van der Spoel <
spoel at xray.bmc.uu.se>:

> Den 2019-06-18 kl. 15:58, skrev Gmx QA:
> > 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
> > /PK
> >
> There are a couple of details indeed, in particular for water. Water may
> bind with oxygen or hydrogens. When your compound provides a hydrogen
> bond acceptor, gmx hbond will compute the hydrogen bond between your
> compound and both H on a water molecule as the same H bond, unless you
> tell it not to with an option -nomerge.
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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