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:
define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
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?