Error performing Martini MD - From CHARMM-GUI creator files

GROMACS version: 2022.04
GROMACS modification: No
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Im using CHARMM-GUI server to create a combination between my transmembrane peptide an a bilayer composed by 3 different phospholipids (POPS, POPC, POPE). Once i already want to perform my MD according to protocol obtained from the README file, minimization soft-core crash and cant go ahead. The error that appears correspond to :

Fatal error: There are perturbed non-bonded pair interactions beyond the pair-list cutoff of 2.1 nm, which is not supported. This can happen because the system is unstable or because intra-molecular interactions at long distances are excluded. If the latter is the case, you can try to increase nstlist or rlist to avoid this.The error is likely triggered by the use of couple-intramol=no and the maximal distance in the decoupled molecule exceeding rlist.

The same README file suggest changing rvdw and rcoulomb if that error appears. But still failing by the same error

If you encountered “There are 1 perturbed non-bonded pair interaction …” error message,
please modify rvdw and rcoulomb values from 1.1 to 2.0 in the step6.0_minimization.mdp file.

Im adding Soft-core Minimization file content, in case you notice something out of place or wrong :

Soft-Core Minimization file

define = -DFLEXIBLE
integrator = steep
tinit = 0.0
nsteps = 500000

nstlog = 100
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 2.2
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 2.2

tcoupl = v-rescale
tc-grps = protein membrane solute
tau_t = 1.0 1.0 1.0
ref_t = 309.65 309.65 309.65

; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

gen_vel = yes
gen_temp = 309.65
gen_seed = 6924814221

;soft-core-minimization so that single precision GROMACS works here
; Free energy parameters
free-energy = yes
init-lambda = 0.01
sc-alpha = 4
sc-power = 2
sc-coul = yes
nstdhdl = 0
couple-moltype = system
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw-q
; in the final state, both are off.
couple-lambda1 = none
couple-intramol = yes

refcoord_scaling = all



Generated by CHARMM-GUI (

1) Use Gromacs 5.1 or newer to run these simulations



step6.0 - soft-core minimization

If you encountered “There are 1 perturbed non-bonded pair interaction …” error message,

please modify rvdw and rcoulomb values from 1.1 to 2.0 in the step6.0_minimization.mdp file

gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -r step5_charmm2gmx.pdb -p -n index.ndx -maxwarn 1
gmx mdrun -deffnm step6.0_minimization


gmx grompp -f step6.1_minimization.mdp -o step6.1_minimization.tpr -c step6.0_minimization.gro -r step5_charmm2gmx.pdb -p -n index.ndx -maxwarn 1
gmx mdrun -deffnm step6.1_minimization


set cnt = 2
set cntmax = 6

while ( {cnt} <= {cntmax} )
@ pcnt = ${cnt} - 1
if (cnt == 2) then gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_minimization.gro -r step5_charmm2gmx.pdb -p -n index.ndx
gmx grompp -f step6.{cnt}_equilibration.mdp -o step6.{cnt}_equilibration.tpr -c step6.{pcnt}_equilibration.gro -r step5_charmm2gmx.pdb -p -n index.ndx endif gmx mdrun -deffnm step6.{cnt}_equilibration
@ cnt += 1


gmx grompp -f step7_production.mdp -o step7_production.tpr -c step6.6_equilibration.gro -p -n index.ndx
gmx mdrun -deffnm step7_production

Thanks you,