[gmx-users] g_hbond

Carla Jamous carlajamous at gmail.com
Thu Nov 4 11:32:57 CET 2010

Hi Erik,

I tried what you said: I made index groups containing only the atoms
involved in that hbond and ran g_hbond again. The problem didn't persist.
So I wanted to check if I misinterpreted the map: for that, I compared my 4
index files: the one of my concatenated trajectory and the three of the
separate trajectories.
When I look at this comparison table and then at my concatenated hbond map,
the results don't match: for example, the Hbond that has the number 1 in my
concatenated trajectory doesn't appear in my concatenated map (it means that
in my map, next to y=1, nothing appears), however, this same H-bond (same
number of atoms involved) exists in my first and my third trajectories'
index files. So please could you explain how to interpret the map and if
next to some y value in my map, nothing appears, is this value taken into
account in my index file?

Thank you,

On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> Erik Marklund skrev 2010-11-02 20.33:
>  Carla Jamous skrev 2010-11-02 17.35:
>>> Hi to all,
>>> I'm sorry I'm asking again a question I asked a week ago but I still
>>> haven't found my answer:
>>> I concatenated 3 trajectories of 3 different molecules (that have the
>>> same number of atoms) with trjcat: trjcat -settime
>>> Then I ran g_hbond on the concatenated trajectory, I got an index.ndx
>>> file that contains an H-bond between the Thr121 of my protein and an atom N2
>>> of my ligand. This H_bond  figures in the 3 trajectories when I look at the
>>> hbmap of my concatenated trajectory.
>>> On the other hand, I ran g_hbond on each of the 3 different trajectories.
>>> This H_bond doesn't exist in the index files of two of my trajectories. So
>>> it doesn't match the result I get with my concatenated trajectory.
>>> To be sure that this result is right, I calculated the angle and the r of
>>> my H-bond in VMD during each of the 3 trajectories and the results indicate
>>> that this H-bond doesn't exist (I consider that r must be < or equal to 0.35
>>> nm and angle < or equal to 30 degrees).
>>> Please can anyone tell me why the results of g_hbond in my concatenated
>>> trajectory don't match the results of g_hbond on each of my trajectories?
>>> Thank you
>>> Carla
>> Hi,
>> This sounds strange. Could you file a bugzilla and either upload the
>> trajectories+tpr, or, if the files are huge, make them available my other
>> means? I need to have a closer look, perhaps through a debugger.
>>  A simple test you could do yourself is to make index groups containing
> only the atoms involved in that hbond and run g_hbond again. If the problem
> persists, then it looks like a bug. If not, then I still can't rule out
> misinterpretation of the matrix.
> Erik
> --
> -----------------------------------------------
> 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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