see article

https://manual.gromacs.org/documentation/current/reference-manual/analysis/hydrogen-bonds.html

Dear Andresa Messias da Silva ,

I don't know if there is a more formal way to do this, but I did something like this a long time ago:

i) after running the simulation, create a fake topology with the Cl atom renamed as N;

ii) generate e "fake.tpr" file;

iii) run the hbond tool with this new .tpr file.

Optionally, you can convert the trajectory to .pdb and try Travis Analyzer. If I remember correctly, it asks which atoms should be considered as donors/acceptors.

Hope it helps!

Felippe

The gmx hbond command accepts only the OH and NH groups as donors, and the O and N atoms as acceptors. Felippe Colombari 's suggestion is interesting, but first you must decide if the group you want to calculate hbond is a donor or an acceptor, to classify it correctly according to the gromacs rules.

I have attached the command manual

https://manual.gromacs.org/documentation/current/onlinehelp/gmx-hbond.html#gmx-hbond

best regards