Remove water from hydrophobic core

[tanjim_ibl]

GROMACS version: 2025.2
GROMACS modification: Yes

I got a membrane from CHARMM-GUI and removed water from the box. Then I added some peptides over the membrane and resolvated the membrane. Now, there are water molecules in the hydrophobic core. It’s practically impossible to remove the water manually from .gro file and keep up with updating the topology file. Is there any solution to this?
You can clearly see in the image that the water is in the hydrophobic core.

[Karis]

There are a few other posts addressing similar issues such as the posts here, here and here, have you tried out some of these suggestions?