Suggestions on How to Push Lipids Closer to Protein in Membrane

GROMACS version: 2020.5
GROMACS modification: No

Hi all, I am a somewhat new user to GROMACS. I am accustomed to running simulations on membrane systems using files provided from CHARMM-GUI membrane builder. I am currently struggling to run simulations on a system containing an ion channel protein in the membrane. After building the system with CHARMM-GUI, there is a noticeable vacuum right around the protein circumference when viewed from the top or bottom plane. This causes water to flow into these crevices in the membrane as I follow the relaxation steps.

I would like to know if there is an approach I can take to push the surrounding lipids closer to the protein. Better yet, if there is a tool that can allow me to build a membrane around a protein of choice. My system settings are as provided in CHARMM-GUI with this kind of system, here is a sample of what an NPT mdp file:

integrator = md
dt = 0.001
nsteps = 125000
nstxtcout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
tcoupl = berendsen
tc_grps = SOLU MEMB SOLV
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
nstcomm = 100
comm_mode = linear
comm_grps = SOLU MEMB SOLV

The only changes are found in the number of steps, and the removal of pressure parameters when the the simulation switches to NVT.

Please let me know if there is any other information I could provide that could help to solve the problem, I am unsure of how to upload an image of the system on here. Any help will be appreciated! Thank you.