[gmx-users] implementation of hydrogen-bonding calculation

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 5 09:43:01 CET 2003

On Fri, 2003-12-05 at 09:21, Marc Baaden wrote:
> Hi David,
> >>> David said:
>  >> > 	In the Gromacs mannual, the criteria for hydrogen-bonding is
>  >> > 	1. donor-acceptor distance < 3.5 \AA and
>  >> > 	2. acceptor-donor-hydrogen angle < 60 degree
>  >> [..]
>  >> This has been fixed in the next release. Now we can reproduce hbonding
>  >> studies from the literature. We hope to put out a 3.2.0 beta version in
>  >> the weekend and a final one before christmas.
> this is interesting. Can you comment a bit more on this ? How should
> one do a proper h-bond analysis with gmx 3.1.4 ? Or asking the other
> way round how useful are current g_hbond results (standard parameters) ?
It depends what you compare to. Our first implementation was meant to be
roughly comparable to DSSP. I do not recall why we used the H-A distance
rather than D-A, although I vaguely recall that it is used elsewhere
too. In the new version it is an option, with D-A being the default.

When I quite recently tried to reproduce literature results of water
simulation and found some oddities, I looked into all this stuff. The
number of hbonds can now be reproduced exactly compared to literature
values. But there is more... In the "old" g_hbond, hbonds with multiple
possible hydrogens connecting D and A (e.g. for water-water there are
four Hs that can make a hbond between a given D and A) are treated as
different hbonds. This is also contrary to what's used in the
literature, and it now is an option to define these as separate or merge
them to one hbond. This merging does not affect the number of hbonds,
but is does affect the hbond autocorrelation function.

Finally I built in a feature to use g_hbond for contact analysis, not
looking at hbonds, but just atom-atom contacts within two groups
(including contact autocorrelation).

> Thanks,
> MArc
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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