# H-bond calculation

**URL:** <https://gromacs.bioexcel.eu/t/h-bond-calculation/7124>\
**Category:** User discussions\
**Tags:** gmx-hbond\
**Created:** [September 2, 2023, 7:16pm UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124 "2023-09-02T19:16:38Z")\
**Posts on this page:** 1\
**Showing post:** 3

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**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\
**Post date:** [September 3, 2023, 12:43pm UTC](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124/3 "2023-09-03T12:43:05Z")

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Please define **different groups** in your **index file** (\*.ndx) and make sure you’re using the latest GROMACS version, **2023.2**. Here is a discussion that might be helpful to you:

> [@Hbond for docked protein-protein complex](https://gromacs.bioexcel.eu/t/hbond-for-docked-protein-protein-complex/3529):
>
> GROMACS version: 2020.2 GROMACS modification: No Hi, I have a docked protein-protein complex and performed md simulations. I want to make a hydrogen bond study between these 2 proteins using gmx hbond ( gmx hbond -f md.xtc -s md.tpr -num hbnum\_Pro-Pro.xvg and issuing Protein , Protein (same atom numbers for both)) however, I believe this way I’m looking at intraprotein H bonds instead of interprotein H bonds, right? The md simulation was run using a pdb file with the two protein chains in it…

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_[View the full topic](https://gromacs.bioexcel.eu/t/h-bond-calculation/7124)._