# How to estimate H-Bond energy in gromacs

**URL:** <https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903>\
**Category:** User discussions\
**Created:** [October 3, 2021, 7:47am UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903 "2021-10-03T07:47:53Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Liujy](https://avatars.discourse-cdn.com/v4/letter/l/ac91a4/32.png) [@Liujy](https://gromacs.bioexcel.eu/u/Liujy)\
**Post date:** [October 3, 2021, 7:47am UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/1 "2021-10-03T07:47:53Z")

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I would like to quantify H-Bond energy and apolar solvation energy for my system (a protein chain). The latter can be estimated by g\_mmpbsa. But it seems that the H-Bond energy cannot be estimated either by gmx or by g\_mmpbsa…?  
Is there a method to achieve this?

Many thanks!

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [October 4, 2021, 8:10am UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/2 "2021-10-04T08:10:29Z")

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The quantities you are asking for are now well defined. Those appear in simplified models that decompose free-energies to be able to compute fre-energies in a faster, simplified way. In reality, interactions between atoms and molecules arise from electrostatic and Van der Waals interactions. Those can not be uniquely decomposed in e.g. H-bond and apolar solvation energies. The energy of and H-bond in e.g. water depends on the definition. If you have very precise definitions for the quantities you are interested in, you might be able to compute them.

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**Author:** ![Liujy](https://avatars.discourse-cdn.com/v4/letter/l/ac91a4/32.png) [@Liujy](https://gromacs.bioexcel.eu/u/Liujy)\
**Post date:** [October 4, 2021, 1:36pm UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/3 "2021-10-04T13:36:35Z")

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Thanks very much :)  
I use Gromacs’ built-in criterion to determine hydrogen bonds. How to compute the energy?

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**Author:** ![gongrehk](https://avatars.discourse-cdn.com/v4/letter/g/b5ac83/32.png) [@gongrehk](https://gromacs.bioexcel.eu/u/gongrehk)\
**Post date:** [October 12, 2021, 8:59am UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/4 "2021-10-12T08:59:09Z")

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Hi, Liujy!  
Have you found the way to estimate H-Bond energy? I am also curious about this problem.I tried to estimate the H-Bond energy to be the electrostatic energy between the Hydrogen and acceptor atom ,but the strength is too large( around 200 kJ/mol).

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**Author:** ![Liujy](https://avatars.discourse-cdn.com/v4/letter/l/ac91a4/32.png) [@Liujy](https://gromacs.bioexcel.eu/u/Liujy)\
**Post date:** [October 12, 2021, 10:23am UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/5 "2021-10-12T10:23:14Z")

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I did not find a way to estimate H-Bond energy… It seems that we cannot estimate purely H-Bond energy by Gromacs if there are other types of interaction between residues.

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**Author:** ![gongrehk](https://avatars.discourse-cdn.com/v4/letter/g/b5ac83/32.png) [@gongrehk](https://gromacs.bioexcel.eu/u/gongrehk)\
**Post date:** [October 13, 2021, 12:48pm UTC](https://gromacs.bioexcel.eu/t/how-to-estimate-h-bond-energy-in-gromacs/2903/6 "2021-10-13T12:48:51Z")

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Thanks for you information! Good luck!