[gmx-developers] index mistakes in the output file of gmx hbond -hbn

叶永峰 yeyongfeng at sjtu.edu.cn
Tue Dec 22 15:13:39 CET 2020

Dear sir/madam,
I find mistakes in the output file of gmx hbond -hbn when I run a simulation where I want to know the hydrogen bonds between 2 kinds of moleculars, H2O and glycerol.
The command I use to analyze the hydrogen bonds is:
echo 0 1 | gmx hbond -f frame10.gro -s md_1.tpr -n traj0.ndx -a 20 -r 0.31 -hbn wg0.ndx
Here is two lines of the indexes under [ hbonds_water_glycerol ] in wg0.ndx:

44533  44534  25652
44533  44534  29978

By comparing the indexes and the ones in the file frame10.gro, I can know that the order of the indexes above corresponds the order of donor-Hydrogen atom-acceptor. Firstly, it may occurs that the same donor-Hydrogen atom forms 2 different hydrogen bonds with 2 acceptors (sometimes 3 in the wg0.ndx file) due to the geometric criterion, I find too many of them. Secondly by calculating the angles of Hydrogen atom-donor-acceptor which demand <20°, I find the second line above should be: 44533  44535  29978(see the figure attached).
I use gromacs2018.4 to run the md and analyze the H-bonds, and similar issues can be found using gromacs 5.0.7 and gromacs 2020.4. The relevant files and the figure showing the angles I calculate manually are can be downloaded in https://gitlab.com/gromacs/gromacs/-/issues/3837.

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