Compute hydrogen bonds for each frame

User discussions
1

GROMACS version: 2024.1
GROMACS modification: No

Hello!

I would like to generate a file containing which atoms are involved in hydrogen bond for each frame of the simulation. How is it possible? I tried gmx hbond -hbn and -hbm but it isn’t exacly what I want.

Thank you!

2

Hi,

You can first make an index file for the specific atoms that you are interested in. Use gmx make_ndx command in gromacs and then used the gmx hbond with -n index.ndx in it. When prompted, select the groups that you are interested in.

3

Hi,

I tried creating an index file and then computing the hydrogen bonds with hbond-legacy. I tried -hbn, -hbm and -dan, but none of these gives exactly what I want… For clarification, I’m analyzing the hydrogen bonds between a solute and a solvent. I wanted to have the information on which atoms form an hydrogen bond for each frame.