LJ-PME with user defined non-bonded parameters

GROMACS version:5.15
GROMACS modification: No

I’m trying to calculate Absolute Binding Free Energy (ABFE) using gromacs, when I finished all input file and run simulations, I got some NOTE from gromacs like this below:

NOTE2 [file …/…/MDP/PROD/prod.01.mdp]:
** You are using geometric combination rules in LJ-PME, but your non-bonded C6 parameters do not follow these rules. This will introduce very small errors in the forces and energies in your simulations. Dispersion correction will correct total energy and/or pressure for isotropic systems, but not forces or surface tensions.**

Can someone help me to find what’s going on here in my MDP file and give me some advides that how to solve this issue?

Best regard~

my MDP file is as follow:

==================================================================
;====================================================
; Production simulation
;====================================================

;----------------------------------------------------
; RUN CONTROL
;----------------------------------------------------
integrator = sd ; stochastic leap-frog integrator
nsteps = 2500000 ; 2 * 2,500,000 fs = 5000 ps
dt = 0.002 ; 2 fs
comm-mode = Linear ; remove center of mass translation
nstcomm = 100 ; frequency for center of mass motion removal

;----------------------------------------------------
; OUTPUT CONTROL
;----------------------------------------------------
nstxout = 0 ; don’t save coordinates to .trr
nstvout = 0 ; don’t save velocities to .trr
nstfout = 0 ; don’t save forces to .trr
nstxout-compressed = 1000 ; xtc compressed trajectory output every 1000 steps (2 ps)
compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file
nstlog = 1000 ; update log file every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstcalcenergy = 100 ; calculate energies every 100 steps

;----------------------------------------------------
; BONDS
;----------------------------------------------------
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; hydrogens only are constrained
lincs_iter = 1 ; accuracy of LINCS (1 is default)
lincs_order = 4 ; also related to accuracy (4 is default)
lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default)
continuation = yes

;----------------------------------------------------
; NEIGHBOR SEARCHING
;----------------------------------------------------
cutoff-scheme = Verlet
ns-type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs (default is 10)
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
pbc = xyz ; 3D PBC

;----------------------------------------------------
; ELECTROSTATICS
;----------------------------------------------------
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
ewald_geometry = 3d ; Ewald sum is performed in all three dimensions
pme-order = 6 ; interpolation order for PME (default is 4)
fourierspacing = 0.10 ; grid spacing for FFT
ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb

;----------------------------------------------------
; VDW
;----------------------------------------------------
vdw-type = PME
rvdw = 1.0
vdw-modifier = Potential-Shift
ewald-rtol-lj = 1e-3
lj-pme-comb-rule = Geometric
DispCorr = EnerPres

;----------------------------------------------------
; TEMPERATURE & PRESSURE COUPL
;----------------------------------------------------
tc_grps = System
tau_t = 1.0
ref_t = 300
pcoupl = Parrinello-Rahman
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2 ; time constant (ps)
ref_p = 1.0 ; reference pressure (bar)
compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1)

;----------------------------------------------------
; VELOCITY GENERATION
;----------------------------------------------------
gen_vel = no ; Velocity generation is off (if gen_vel is ‘yes’, continuation should be ‘no’)
gen_seed = -1 ; Use random seed
gen_temp = 300

;----------------------------------------------------
; FREE ENERGY CALCULATIONS
;----------------------------------------------------
free-energy = yes
couple-moltype = LIG
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = no
separate-dhdl-file = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
init-lambda-state = 1
coul-lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
nstdhdl = 100
calc-lambda-neighbors = -1