Hbond wrong number possible bonds

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No
I simulated a mixture of diethylene glycol, triethylene glycol, and tip4p2005 water with OPLSAA. I ran gmx hbond to find the intramolecular hydrogen bonding within diethylene glycol. From an index file I made there are two groups from the same molecule: one is the hydroxy oxygens and hydrogens, the other is the ether oxygen. It says there are three possible bonds. I figure there should be two, one from each hydroxy group to the ether oxygen. Any insight is appreciated.

here’s the output:
Specify 2 groups to analyze:
Selected 5: 'PEG_OA_PEG_HA_&DEG&r_1’
Selected 6: 'PEG_OE&DEG&r_1’
Checking for overlap in atoms between PEG_OA_PEG_HA&DEG&r_1 and PEG_OE&DEG&r_1
Calculating hydrogen bonds between PEG_OA_PEG_HA&DEG&r_1 (4 atoms) and PEG_OE&DEG&_r_1 (1 atoms)
Found 2 donors and 3 acceptors

Will do grid-search on 8x8x8 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 8 threads.
Average number of hbonds per timeframe 0.028 out of 3 possible

2

Diethylene Glycol has two OHs and and one =O, possible combinations,

  • OH1-OH2
  • OH1-(=O)
  • OH2-(=O)
3

Since the OHs are in the same group shouldn’t it ignore this combination as it is supposed to be looking for hbonding between the two groups not within them? I don’t want it to include the OH-OH bond, is there a way to remove it?

Is there a way to select one group to only be the donor and the other to only be the acceptor?

4

Possibly different ways you can do that. You may try to calculate HB between OH groups separately and subtract from total HB count.