Question about hydrogen bonding calculation

[Maria Thereza]

Hello everyone!

I am interested on the intramolecular hydrogen bonds formed within my system (a molecule of sugar + water). I managed to get information on each intramolecular bond that was formed with:

counts_sorbitol_intramolecular = hbonds_sorbitol_intramolecular.count_by_ids()
lines = []

for donor, hydrogen, acceptor, count in counts_sorbitol_intramolecular:
    d, h, a = u_sorbitol.atoms[donor], u_sorbitol.atoms[hydrogen], u_sorbitol.atoms[acceptor]
    lines.append(f"{d.resname}-{d.resid}-{d.name}-{d.index}\t{h.resname}-{h.resid}-{h.name}-{h.index}\t{a.resname}-{a.resid}-{a.name}-{a.index}\tcount={count}")

for line in sorted(lines):
    print(line)

My first question is about the "count" part. If the count is equal to 1, my first thought is that it is formed 1 time throughout the simulation time. However, is it possible that it is a persistent hydrogen bond that is formed once and stays until the end of the simulation?

Also, I wanted to verify this by printing, for each frame, which are exactly the intramolecular hydrogen bonds present. Is it possible to do this? The count_by_time() method only contains the number of hydrogen bonds per timestep if I understood correctly, and I think count_by_ids doesn't provide information for each frame - only for the whole simulation.

Thank you for your support!

Best,

Maria

[Micaela Matta]

Hi Maria,

what options did you use when calling HydrogenBondAnalysis?
What do you see when looking at the hbonds.results.hbonds array (https://userguide.mdanalysis.org/stable/examples/analysis/hydrogen_bonds/hbonds.html#Accessing-the-results)?  

If you are only looking at intramolecular HBs  in a single sorbitol molecule, I would say it's possible to have the same HB throughout the trajectory (it would mean that your molecule is not changing conformation). Hard to elaborate more as I don't have enough information on the system..

Hope this helps,

Micaela