# Gmx H-bond analysis help

**URL:** <https://gromacs.bioexcel.eu/t/gmx-h-bond-analysis-help/6046>\
**Category:** User discussions\
**Created:** [March 25, 2023, 2:53pm UTC](https://gromacs.bioexcel.eu/t/gmx-h-bond-analysis-help/6046 "2023-03-25T14:53:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\
**Post date:** [March 25, 2023, 2:53pm UTC](https://gromacs.bioexcel.eu/t/gmx-h-bond-analysis-help/6046/1 "2023-03-25T14:53:29Z")

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Hello gromacs users,

For a peptide structure generated by simulations on gromacs; I see no hydrogen bond occupancy (0%) between two sites 1 and 2 when I apply gmx hbond analysis on this one structure. Attempted default cutoff and higher values.  
However, when I load the molecule on Pymol, I clearly see a H-bond between those two sites with cut off distance of 2.7 A. I do not understand where am I going wrong.

Any insight would be appreciated!

Many thanks,  
Neena

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [March 26, 2023, 5:17pm UTC](https://gromacs.bioexcel.eu/t/gmx-h-bond-analysis-help/6046/2 "2023-03-26T17:17:15Z")

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> [@Neena](#):
>
> I clearly see a H-bond between those two sites with cut off distance of 2.7 A.

To what distance does this correspond? The H-acceptor or the donor-acceptor? Note that GROMACS uses a donor-acceptor distance, as well as an angle criterion. What species (chemical groups) are involved in the interaction that you are seeing?