How to compute the number of hydrogen bonds per molecule in a pure water system: gmx hbond

User discussions
,
1

GROMACS version: 2022
GROMACS modification: No

Hi,
I’m trying to compute the number of hydrogen bonds per water molecule in a pure water system as my control for another simulation. But every time I run gmx hbond with the -num flag, I get an output value around 11700. I thought I could divide this number by the number of water molecules in my system (7029), but I get the a value around 1.6. I thought the problem could be that gmx hbond was merging the equivalent atoms, but the value didn’t change at all when I used the -nomerge flag.

I’m using it as follows:

gmx hbond -f md_skip15.xtc -s md.tpr -num hbondnum.xvg -dist hbonddist.xvg -ang hbondang.xvg -n index.ndx -b 200000  

gmx hbond -f md_skip15.xtc -s md.tpr -num hbondnum.xvg -dist hbonddist.xvg -ang hbondang.xvg -n index.ndx -b 200000  -nomerge

I’m using SOL as the selection for both groups. I also didn’t get the hbonds.ndx index file nor the .xpm map. I also tried it with gromacs 2023 and got the same exact result.

I’m using the TIP3P water model and the Amber ff99sb-ildn forcefield.

Thanks