H-bond analysis

[lauraf244]

Hello,

i'm trying to calculate the interaction between one N atom of my substrate and the H atom from one molecule of solvent near to it for a LAMMPS MD.
As i can see in the trajectory with vmd and from the rdf analysis this atom "moves from the solvent" to the substrate ending doing a covalent bond with the N of the substrate. The same data si confirmed in the rdf showing a peak at 1.10 A and g(r) 100 for this N-H interaction.
Now i'm using this script to analysis the number of this H-bond (as further proof that this interaction occurs in most of the frames)

import numpy as np
import MDAnalysis as mda
from MDAnalysis.analysis.hydrogenbonds import HydrogenBondAnalysis
import pandas as pd
import matplotlib.pyplot as plt

# Carica l’universo
u = mda.Universe(
    'packmol_liquid_generator/output/opt-DFT+packmol/CPX-menth-acetic-70.xyz',
    'output/liquid/CPX-menth-acetic-70/lmp.xtc',
    guess_bonds=True
)

# Selezioni specifiche
donors_sel = "bynum 1252"       # idrogeno specifico solvente
hydrogens_sel = "bynum 1263"    # stesso idrogeno
acceptors_sel = "bynum 13"      # azoto 13 del substrato

# Setup analisi H-bond
hba = HydrogenBondAnalysis(
    universe=u,
    donors_sel=donors_sel,
    hydrogens_sel=hydrogens_sel,
    acceptors_sel=acceptors_sel,
    d_a_cutoff=5.0,
    d_h_a_angle_cutoff=0.0
)

# Esegui analisi
hba.run(verbose=True)

# Risultati in array e DataFrame
hbonds_array = hba.results.hbonds
hb_df = pd.DataFrame(
    hbonds_array,
    columns=['frame', 'donor_idx', 'hydrogen_idx', 'acceptor_idx', 'distance', 'angle']
)

print(f"Interazioni H-bond totali tra idrogeno 1263 e azoto 13: {len(hb_df)}")

hbonds_per_frame = hb_df.groupby('frame').size()
indices = hbonds_per_frame.index.astype(int)  # conversione esplicita a interi

all_frames = np.arange(len(u.trajectory))
counts_full = np.zeros(len(u.trajectory), dtype=int)
counts_full[indices] = hbonds_per_frame.values

print(f"Media H-bonds/frame (tutti i frame): {counts_full.mean():.2f}")

and i get only these numbers of H-bonds:
Interazioni H-bond totali tra idrogeno 1263 e azoto 13: 23
Media H-bonds/frame (tutti i frame): 0.11.

There is obviously a mismatch but i'm getting crazy to understand why.
I have already checked the connectivity between the atoms indicated in the indexes and i have tried to change the cutoff also, but nothing,

Thank you very much

# Plot
plt.figure(figsize=(8,4))
plt.plot(all_frames, counts_full, color='blue', label='N13 accetta H1263')
plt.xlabel('Frame')
plt.ylabel('Numero di H-bond')
plt.title('H-bond tra idrogeno 1263 (solvente) e azoto 13 (CPX)')
plt.grid(True)
plt.legend()
plt.tight_layout()
plt.show()