# Gromacs hbond problem - 1 frame with high number of hbonds

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002>\
**Category:** User discussions\
**Tags:** analysis-tools, gmx-hbond\
**Created:** [August 10, 2023, 11:30am UTC](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002 "2023-08-10T11:30:44Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Davidb](https://avatars.discourse-cdn.com/v4/letter/d/76d3ee/32.png) [@Davidb](https://gromacs.bioexcel.eu/u/Davidb)\
**Post date:** [August 10, 2023, 11:30am UTC](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002/1 "2023-08-10T11:30:44Z")

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GROMACS version: 2023  
GROMACS modification: Yes - with plumed

Hi,  
I am trying to analyze hbonds between a molecule and a protein. The complex was generated using CHARM-GUI so there is .itp file for the molecule.  
I am using gromacs gmx hbond command with 2 groups I have created (the molecule with 45 atoms and the protein with around 7500 atoms). This is the exact command:  
“gmx\_mpi hbond -f step5\_1.xtc -s step5\_1.tpr -n updated\_index.ndx -num hb1.xvg”

The times are in picoseconds, each frame 50 ps - 501 frames in total.

 ![Screenshot 2023-08-10 134042](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8730ba742de4e98073bd01c1c3c464bf641853c4.png)

Because the number of hydrogen bonds in step 900 (frame 19) looks impossible, I checked it with other program. I used VMD - trajectory tool to analyze the bonds, and this is the result:

 ![Screenshot 2023-08-10 151206](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/12138b408ce90f1f0738e864ca713c8b68c179c1.png)

X axis shows the frame number, and the hydrogen bonds in Y. The number of hbonds are a bit different but I assume that the definitions of hbonds are just different between the programs, and of course not reaching millions.

I tried using gmx hbond on other part of the protein (it is a trimer) with the corresponding molecule, and generally I get the same result. In addition, If I don’t use the corresponding molecule, I see mostly 0 hbonds but in step 600 I see 2 million hydrogen bonds again.

What might be the problem? I prefer to go by gromacs analysis because it is easier to work with .trr files and not xtc - low memory to load long trajectories.

Thank you.  
David.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [August 11, 2023, 5:32pm UTC](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002/2 "2023-08-11T17:32:44Z")

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Hi David,  
Which version of gmx hbond are you using?  
In 2023 there was a bug in gmx hbond that has been fixed in 2023.2  
see release note. [https://manual.gromacs.org/2023.2/release-notes/2023/2023.2.html](https://manual.gromacs.org/2023.2/release-notes/2023/2023.2.html)

Alessandra

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**Author:** ![Davidb](https://avatars.discourse-cdn.com/v4/letter/d/76d3ee/32.png) [@Davidb](https://gromacs.bioexcel.eu/u/Davidb)\
**Post date:** [August 14, 2023, 7:48am UTC](https://gromacs.bioexcel.eu/t/gromacs-hbond-problem-1-frame-with-high-number-of-hbonds/7002/3 "2023-08-14T07:48:00Z")

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I use 2023.2 version so that one should be fixed.