# List of H-bond donors and acceptors

**URL:** <https://gromacs.bioexcel.eu/t/list-of-h-bond-donors-and-acceptors/354>\
**Category:** User discussions\
**Created:** [June 21, 2020, 8:11pm UTC](https://gromacs.bioexcel.eu/t/list-of-h-bond-donors-and-acceptors/354 "2020-06-21T20:11:33Z")\
**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:** [June 21, 2020, 8:11pm UTC](https://gromacs.bioexcel.eu/t/list-of-h-bond-donors-and-acceptors/354/1 "2020-06-21T20:11:33Z")

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GROMACS version: 2019.1  
GROMACS modification: No  
Here post your question

What command should I use with gmx hbond in order to get a list (text file) of H-bond donors and acceptors as a function of trajectory time?  
Why do I need this? To study specifically which H-bonds are fluctuating more during a trajectory (both number and length of H-bonds)

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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:** [June 21, 2020, 10:13pm UTC](https://gromacs.bioexcel.eu/t/list-of-h-bond-donors-and-acceptors/354/2 "2020-06-21T22:13:28Z")

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GROMACS does not have the ability to do this, but I wrote a script that can: [https://osf.io/3wunt/](https://osf.io/3wunt/)

You will need to use the `-hbn` and `-hbm` options in `gmx hbond` to create the H-bonding map and corresponding index files. Then you will need to edit these files as noted in the header of the script (it’s a rather dumb script that I wrote many years ago but have not had the need to improve in any way).