Gmx H-bond analysis help

[Neena]

Hello gromacs users,

For a peptide structure generated by simulations on gromacs; I see no hydrogen bond occupancy (0%) between two sites 1 and 2 when I apply gmx hbond analysis on this one structure. Attempted default cutoff and higher values.
However, when I load the molecule on Pymol, I clearly see a H-bond between those two sites with cut off distance of 2.7 A. I do not understand where am I going wrong.

Any insight would be appreciated!

Many thanks,
Neena

[jalemkul]

@Neena

I clearly see a H-bond between those two sites with cut off distance of 2.7 A.

To what distance does this correspond? The H-acceptor or the donor-acceptor? Note that GROMACS uses a donor-acceptor distance, as well as an angle criterion. What species (chemical groups) are involved in the interaction that you are seeing?