Hydrogen bond file

User discussions
1

GROMACS version:
GROMACS modification: No

Hi everyone,

I used gmx hbond to compute the hydrogen bonds in each frame of the simulation. I got a .ndx file with the data. For the first frame, for example, I have:

[ hbonds_System_frame_0 ]
1 2 1291
1 3 1498
4 6 550
…

I understand these are the atom ids of the simulation. I’d like to know how exactly the atoms are “organized”: who is the donor, the acceptor and the hydrogen in each line?

Thank you in advance!

2

I believe each row is ordered by the donor, hydrogen and acceptor. To check, you can compare the ids to the topology file or coordinate file, and you should find that atom id 2 is a hydrogen, id 1 is the donor it is bonded to and id 1291 would be an acceptor not directly bonded to the hydrogen