[gmx-users] g_hbond

Carla Jamous carlajamous at gmail.com
Thu Nov 11 16:54:53 CET 2010

Hi everyone,

actually Erik is right. My problem is that I wasn't using the "-nomerge"
So g-hbond was printing the wrong number of hydrogen atom and so all my
results were not matching.
Now that I used "-nomerge", all my H-bonds match even in my concatenated

Thanks to all,
It took me a long time to figure it out, thanks for your patience,

On Thu, Nov 11, 2010 at 4:26 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> Hi,
> I'm thinking it *may* have something to do with how search_donors() and the
> -merge flag work. The hydrogen must be part of the index group you provide.
> Nothing strange there. But the hydrogen that is printed to the index file
> may in fact *not* be the hydrogen bonding one if the -merge flag is set
> (default). Would the vanishing h-bonds happen to have donors with multiple
> hydrogens? There are two things you could try: either add all the donor's
> hydrogen to the index group when validating single h-bonds, or use -nomerge
> to generate a complete list of h-bonds and do your validation on that list.
> Erik
> Carla Jamous skrev 2010-11-09 15.08:
>  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
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
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