[gmx-users] g_hbond

Oliver Grant olymacfoogal at gmail.com
Thu Nov 11 11:45:00 CET 2010

Hi Carla,

I've seen this behavior too but I didn't look at the code. I figured with
the hydrogen included it checks the angle too or if the hydrogen is between
the two heavy atoms. So the first pass just looks at distances between donor
and acceptor atoms and doesn't consider that the hydrogen may be completely
on the wrong side of the donor atom.

Did you look at any of the bonds that were left out in the 2nd pass?


On 9 November 2010 14:08, Carla Jamous <carlajamous at gmail.com> wrote:

> Hi everyone,
> I ran g_hbond on a trajectory. When g_hbond asks for two groups in the
> index file, I give:
> group1: "Protein"
> group2: "ligand"
> The output .ndx file contains 44 Hbonds.
> In order to verify my result on each and every Hbond, I ran g_hbond on the
> same trajectory but this time in my index file, I gave atom triplets, so
> when g_hbond asks for two groups, I give for example:
> group1: "a4810_a4811_a1857"
> group2: "a4810_a4811_a1857"
> Surprisingly, 10 of the 44 Hbonds are not found using this method.
> Am I doing something wrong or is there a problem with g_hbond?
> Thank you,
> Carla
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