GROMACS version: 2023
GROMACS modification: Yes - with plumed
Hi,
I am trying to analyze hbonds between a molecule and a protein. The complex was generated using CHARM-GUI so there is .itp file for the molecule.
I am using gromacs gmx hbond command with 2 groups I have created (the molecule with 45 atoms and the protein with around 7500 atoms). This is the exact command:
“gmx_mpi hbond -f step5_1.xtc -s step5_1.tpr -n updated_index.ndx -num hb1.xvg”
The times are in picoseconds, each frame 50 ps - 501 frames in total.
Because the number of hydrogen bonds in step 900 (frame 19) looks impossible, I checked it with other program. I used VMD - trajectory tool to analyze the bonds, and this is the result:
X axis shows the frame number, and the hydrogen bonds in Y. The number of hbonds are a bit different but I assume that the definitions of hbonds are just different between the programs, and of course not reaching millions.
I tried using gmx hbond on other part of the protein (it is a trimer) with the corresponding molecule, and generally I get the same result. In addition, If I don’t use the corresponding molecule, I see mostly 0 hbonds but in step 600 I see 2 million hydrogen bonds again.
What might be the problem? I prefer to go by gromacs analysis because it is easier to work with .trr files and not xtc - low memory to load long trajectories.
Thank you.
David.