How to solve the GROMACS error "One or more water molecules can not be settled" during SMD?

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GROMACS version:2019.6
GROMACS modification: No
How to solve the GROMACS error “One or more water molecules can not be settled” during SMD?
I hope this message finds you well. I’m currently conducting research involving simulating a membrane protein system using GROMACS 2019.6. I have encountered an issue while attempting to perform a ligand pull from the middle of a channel towards the intracellular side.

To provide context, I conducted a 1 microsecond MD simulation using CHARMM-GUI and GROMACS 2019.6 successfully. However, when attempting to apply steered molecular dynamics (SMD) with various parameter settings in the MDP file, I consistently encountered different errors errors during different times of smd run that make the run stop.
Fatal error:
64 particles communicated to PME rank 17 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

In an attempt to troubleshoot, I switched to GROMACS 2018 for the SMD process and make the run time for 4 ns. It ran without any issues but Regrettably, after 4 nanoseconds of simulation, the helical structures within the protein were destabilized and disappeared. so I reduced the rate from 0.001 to 0.0005 and I received this error:
One or more water molecules can not be settled
I am writing to seek your guidance or insights into potential issues causing these errors during the SMD process and the subsequent destabilization of protein structures. Could you kindly advise on potential sources of these problems or provide suggestions on how to troubleshoot this issue effectively? This is the mdp file I used:

title = Umbrella pulling simulation
define = -DPOSRES_Pro -DSTEP6_0
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 2000000
nstcomm = 10
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 500
nstenergy = 5000
nstxout-compressed = 5000
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes
; Single-range cutoff scheme
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = Pro-lig Mem Water_Ions
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = lig
pull_group2_name = Pro
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.001 ; 0.001 nm per ps = 1 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull-group2-pbcatom = 475
pull-pbc-ref-prev-step-com = yes

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Both 64 particles communicated to PME rank 17 are more than 2/3 times the cut-off and one or more water cannot be settled are errors symptomatic of large forces being generated, leading to system instability.

Either this comes from your system independently of SMD (for instance, because the initial minimization was not sufficient), or it is linked to your pulling setup, either too fast pulling, too high harmonic constant, or pulling direction incompatible with smooth motion.

I would have a look at the trajectory, checking if the pulling is smooth and in a direction that makes sense. You can also look in the vicinity of the waters listed in the one or more water cannot be settled error message, as it might be a local geometry/topology problem. Finally, it might be that your system require particularly gentle pulling: decrease speed and/or k and allow for more simulation time.