# Hydrogen bond analysis in MD simulation

**URL:** <https://gromacs.bioexcel.eu/t/hydrogen-bond-analysis-in-md-simulation/12829>\
**Category:** User discussions\
**Created:** [October 24, 2025, 7:06am UTC](https://gromacs.bioexcel.eu/t/hydrogen-bond-analysis-in-md-simulation/12829 "2025-10-24T07:06:36Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![swagat](https://avatars.discourse-cdn.com/v4/letter/s/ea666f/32.png) [@swagat](https://gromacs.bioexcel.eu/u/swagat)\
**Post date:** [October 24, 2025, 7:06am UTC](https://gromacs.bioexcel.eu/t/hydrogen-bond-analysis-in-md-simulation/12829/1 "2025-10-24T07:06:37Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hi everyone! I want to calculate water or ion mediated hydrogen bonds. Please, let me know what can be done for this calculation?

Only hydrogen bond calcuation with side chains, direct hydrogen bonds are available in md tutorials.

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**Author:** ![swagat](https://avatars.discourse-cdn.com/v4/letter/s/ea666f/32.png) [@swagat](https://gromacs.bioexcel.eu/u/swagat)\
**Post date:** [October 25, 2025, 7:27am UTC](https://gromacs.bioexcel.eu/t/hydrogen-bond-analysis-in-md-simulation/12829/2 "2025-10-25T07:27:19Z")

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GROMACS version is 2024.2

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**Author:** ![Caterpillar](https://avatars.discourse-cdn.com/v4/letter/c/aca169/32.png) [@Caterpillar](https://gromacs.bioexcel.eu/u/Caterpillar)\
**Post date:** [October 26, 2025, 5:53pm UTC](https://gromacs.bioexcel.eu/t/hydrogen-bond-analysis-in-md-simulation/12829/3 "2025-10-26T17:53:58Z")

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You could try using the command

> gmx hbond

and seeing if that can solve your problem.

Documentation is here: [gmx hbond - GROMACS 2025.3 documentation](https://manual.gromacs.org/current/onlinehelp/gmx-hbond.html)