# How to compute the number of hydrogen bonds per molecule in a pure water system: gmx hbond

**URL:** <https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244>\
**Category:** User discussions\
**Tags:** analysis-tools, gmx-hbond\
**Created:** [February 7, 2024, 2:29pm UTC](https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244 "2024-02-07T14:29:59Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![TGaziri](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tgaziri/32/5191_2.png) [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\
**Post date:** [February 7, 2024, 2:29pm UTC](https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244/1 "2024-02-07T14:29:59Z")

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GROMACS version: 2022  
GROMACS modification: No

Hi,  
I’m trying to compute the number of hydrogen bonds per water molecule in a pure water system as my control for another simulation. But every time I run `gmx hbond` with the `-num` flag, I get an output value around 11700. I thought I could divide this number by the number of water molecules in my system (7029), but I get the a value around 1.6. I thought the problem could be that `gmx hbond` was merging the equivalent atoms, but the value didn’t change at all when I used the `-nomerge` flag.

I’m using it as follows:

```auto
gmx hbond -f md_skip15.xtc -s md.tpr -num hbondnum.xvg -dist hbonddist.xvg -ang hbondang.xvg -n index.ndx -b 200000  

gmx hbond -f md_skip15.xtc -s md.tpr -num hbondnum.xvg -dist hbonddist.xvg -ang hbondang.xvg -n index.ndx -b 200000 -nomerge

```

I’m using SOL as the selection for both groups. I also didn’t get the hbonds.ndx index file nor the .xpm map. I also tried it with gromacs 2023 and got the same exact result.

I’m using the TIP3P water model and the Amber ff99sb-ildn forcefield.

Thanks

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<div class="post-metadata">

**Author:** ![Yildiz](https://avatars.discourse-cdn.com/v4/letter/y/df788c/32.png) [@Yildiz](https://gromacs.bioexcel.eu/u/Yildiz)\
**Post date:** [December 3, 2025, 1:47pm UTC](https://gromacs.bioexcel.eu/t/how-to-compute-the-number-of-hydrogen-bonds-per-molecule-in-a-pure-water-system-gmx-hbond/8244/2 "2025-12-03T13:47:08Z")

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Hello, I have been having some problems with the calculating h-bonds per molecule as well. I have been searching the forum for answers but couldn’t find any. I was wondering did you resolve this issue?