GROMACS version: 2022.5 with CP2K 2023.1
GROMACS modification: No
While running grompp to create a tpr file for QM/MM simulation below warning regarding constraints is displayed.
WARNING 1 [file qmmm.mdp]:
Your QM subsystem has a lot of constrained bonds. They probably have been
generated automatically. That could produce an artifacts in the
simulation. Consider constraints = none in the mdp file.
When using constraints = none in the mdp file another warning is shown.
WARNING 1 [file qmmm.top, line 47]:
The bond in molecule-type Protein_chain_B between atoms 45 OG and 46 HG
has an estimated oscillational period of 9.0e-03 ps, which is less than 5
times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option.
Can anyone help me on what is the issue using h-bond constraints and how can I proceed further.