Cannot compile tpr file for CP2K QM/MM simulation with constraints = h-bonds

User discussions
1

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.

2

Did you ever figure it out? I have the same issue.

3

Without h-bond constraints you need a time-step of about 0.5 fs. You will anyhow need this if the QM region includes hydrogens.