Keep water away from the hydrophobic core during equilibration of membrane + inserted peptide

GROMACS version: 2021 (but relate to any version)
GROMACS modification: no

With CHARMM-gui I created a solvated membrane bilayer with helix peptide inserted in transmembrane orientation.
Now I need to equilibrate system, but not allowing water to insert in vacuum parts between peptide and lipids.
CHARMM-gui output six equilibration *.mdp files with “define” option for fixing force constant for protein backbone, sidechains and dihedrals, but with no item for fixing water. For example, in step6.1_equilibration.mdp:


On the other side, in step6.1_equilibration.INP file, one can find line which relate to that:

set wforce = 2.5 ! force constant to keep the water molecules away from the hydrophobic core

Now, during equlibration with GROMACS, I don’t use *.inp file.

Question: How to implement wforce constant in equilibration with gromacs?


It is not straightforward to do in GROMACS what CHARMM can do rather easily on a script-based level, hence why you do not get this option when generating inputs from CHARMM-GUI. To keep water out of the bilayer, you would need to implement flat-bottom restraints, which requires both topology and coordinate file manipulation. Equilibrate without it, and if you get any water leaking into the membrane, there are other ways to deal with it, but I would avoid trying to directly replicate the CHARMM approach.

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