I am building a membrane–drug system using the CHARMM-GUI Membrane Builder (Protein/Membrane System). I have uploaded a PDB file of a small-molecule drug and placed it above the membrane. CHARMM-GUI generates input files for GROMACS, including position restraints. However, during the equilibration process, the drug fails to stay on top of the membrane and drifts away, likely due to weak positional restraints applied by default.
I would like to increase the positional restraint force constant on the drug atoms to 1000 kJ/mol/nm² throughout all equilibration steps (step6.1 to step6.6) to ensure the drug remains close to the membrane surface.
Is this method correct?