Fatal error, depending on absolute position

GROMACS version:2021.4
GROMACS modification: No

Hi,
So I did a little test with a simple ethane->methanol free energy system.
Turns out I get: “Fatal error: There are 110 perturbed non-bonded pair interactions beyond
the pair-list cutoff”
interestingly, if I do the same simulation, using the same input files, the ONLY difference
being the absolute position of the single molecule I use here, then the job finishes
gracefully.
This is obviously something that should not happen - the input files are rather small, so
they are included below as text.

to reproduce the issue, say:
gmx grompp -f md0.mdp -c em.pdb -p fe.top -o fe0.tpr -maxwarn 1
gmx mdrun -v -deffnm fe0 -c fe0-out.pdb

and then, again, with the shifted molecule coords:
gmx grompp -f md0.mdp -c ems.pdb -p fe.top -o fe0s.tpr -maxwarn 1
gmx mdrun -v -deffnm fe0s -c fe0s-out.pdb

If anybody can reproduce this, or suggest a solution, please let me know!
thanks
Michael

=== md0.mdp ===========================================
integrator = md
dt = 0.00001
nsteps = 0
comm-grps = System
comm-mode = Linear
;
nstxout = 1
nstvout = 0
nstfout = 0
nstlog = 1
nstenergy = 1
;
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.1
cutoff-scheme = Verlet
;
coulombtype = PME
rcoulomb = 0.9
vdw_type = cut-off
rvdw = 0.9
DispCorr = no
;
constraints = hbonds
;
free-energy = yes
init-lambda-state = 0
delta-lambda = 0
fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
calc-lambda-neighbors = -1
sc-alpha = 0.5
sc-r-power = 6
sc-power = 2
sc-sigma = 0.3
nstdhdl = 100
dhdl-derivatives = yes
separate-dhdl-file = yes
;
continuation = yes

=== fe,top ======================================================
[ defaults ]
1 2 yes 0.5 0.8333

[ atomtypes ]
c3 c3 0.00000 0.00000 A 3.39771e-01 4.51035e-01
hc hc 0.00000 0.00000 A 2.60018e-01 8.70272e-02
h1 h1 0.00000 0.00000 A 2.42200e-01 8.70272e-02
oh oh 0.00000 0.00000 A 3.24287e-01 3.89112e-01
ho ho 0.00000 0.00000 A 5.37925e-02 1.96648e-02
du du 0.00000 0.00000 A 0.25 0.000000

[ moleculetype ]
MUT 3

[ atoms ]
1 c3 1 MUT C1 1 -0.068100 12.01000 c3 0.033000 12.01000 ; both same 1 1
2 hc 1 MUT H11 2 0.022700 1.00800 h1 0.052100 1.00800 ; both same 2 2
3 hc 1 MUT H12 3 0.022700 1.00800 h1 0.052100 1.00800 ; both same 3 3
4 hc 1 MUT H13 4 0.022700 1.00800 h1 0.052100 1.00800 ; both same 4 4
5 c3 1 MUT C2 5 -0.068100 12.01000 du 0.000000 12.01000 ; only 0 5
6 hc 1 MUT H21 6 0.022700 1.00800 du 0.000000 1.00800 ; only 0 6
7 hc 1 MUT H22 7 0.022700 1.00800 du 0.000000 1.00800 ; only 0 7
8 hc 1 MUT H23 8 0.022700 1.00800 du 0.000000 1.00800 ; only 0 8
9 du 1 MUT O1 9 0.000000 16.00000 oh -0.398300 16.00000 ; only 1 5
10 du 1 MUT HO 10 0.000000 1.00800 ho 0.209000 1.00800 ; only 1 6

[ bonds ]
1 2 1 1.0970e-01 3.1455e+05 1.0970e-01 3.1455e+05 ; both 1-2 1-2
1 3 1 1.0970e-01 3.1455e+05 1.0970e-01 3.1455e+05 ; both 1-3 1-3
1 4 1 1.0970e-01 3.1455e+05 1.0970e-01 3.1455e+05 ; both 1-4 1-4
1 5 1 1.5380e-01 1.9456e+05 ; only 0 1-5
5 6 1 1.0970e-01 3.1455e+05 ; only 0 5-6
5 7 1 1.0970e-01 3.1455e+05 ; only 0 5-7
5 8 1 1.0970e-01 3.1455e+05 ; only 0 5-8
1 9 1 1.4230e-01 2.4552e+05 ; only 1 1-5
9 10 1 9.7300e-02 4.7154e+05 ; only 1 5-6

[ pairs ]
2 6 1 ; only 0 2-6
2 7 1 ; only 0 2-7
2 8 1 ; only 0 2-8
3 6 1 ; only 0 3-6
3 7 1 ; only 0 3-7
3 8 1 ; only 0 3-8
4 6 1 ; only 0 4-6
4 7 1 ; only 0 4-7
4 8 1 ; only 0 4-8
2 10 1 ; only 1 2-6
3 10 1 ; only 1 3-6
4 10 1 ; only 1 4-6

[ angles ]
1 5 6 1 1.0980e+02 3.9162e+02 ; only lambda=0 1-5-6
1 5 7 1 1.0980e+02 3.9162e+02 ; only lambda=0 1-5-7
1 5 8 1 1.0980e+02 3.9162e+02 ; only lambda=0 1-5-8
2 1 3 1 1.0758e+02 3.2635e+02 1.0846e+02 3.2468e+02 ; both 2-1-3 2-1-3
2 1 4 1 1.0758e+02 3.2635e+02 1.0846e+02 3.2468e+02 ; both 2-1-4 2-1-4
2 1 5 1 1.0980e+02 3.9162e+02 ; only lambda=0 2-1-5
3 1 4 1 1.0758e+02 3.2635e+02 1.0846e+02 3.2468e+02 ; both 3-1-4 3-1-4
3 1 5 1 1.0980e+02 3.9162e+02 ; only lambda=0 3-1-5
4 1 5 1 1.0980e+02 3.9162e+02 ; only lambda=0 4-1-5
6 5 7 1 1.0758e+02 3.2635e+02 ; only lambda=0 6-5-7
6 5 8 1 1.0758e+02 3.2635e+02 ; only lambda=0 6-5-8
7 5 8 1 1.0758e+02 3.2635e+02 ; only lambda=0 7-5-8
1 9 10 1 1.0726e+02 4.1003e+02 ; only lambda=1 1-5-6
2 1 9 1 1.1026e+02 5.2300e+02 ; only lambda=1 2-1-5
3 1 9 1 1.1026e+02 5.2300e+02 ; only lambda=1 3-1-5
4 1 9 1 1.1026e+02 5.2300e+02 ; only lambda=1 4-1-5

[ dihedrals ]
2 1 5 6 9 0.00 0.50208 3 ; only lambda=0 2-1-5-6 3
2 1 5 7 9 0.00 0.50208 3 ; only lambda=0 2-1-5-7 3
2 1 5 8 9 0.00 0.50208 3 ; only lambda=0 2-1-5-8 3
3 1 5 6 9 0.00 0.50208 3 ; only lambda=0 3-1-5-6 3
3 1 5 7 9 0.00 0.50208 3 ; only lambda=0 3-1-5-7 3
3 1 5 8 9 0.00 0.50208 3 ; only lambda=0 3-1-5-8 3
4 1 5 6 9 0.00 0.50208 3 ; only lambda=0 4-1-5-6 3
4 1 5 7 9 0.00 0.50208 3 ; only lambda=0 4-1-5-7 3
4 1 5 8 9 0.00 0.50208 3 ; only lambda=0 4-1-5-8 3
2 1 9 10 9 0.00 0.47279 3 ; only lambda=1 2-1-5-6 3
3 1 9 10 9 0.00 0.47279 3 ; only lambda=1 3-1-5-6 3
4 1 9 10 9 0.00 0.47279 3 ; only lambda=1 4-1-5-6 3

[ dihedrals ]

[ exclusions ]
9 5 6 7 8
10 5 6 7 8

[ system ]
system

[ molecules ]
MUT 1

=== em.pdb ===========================================
CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 MUT 1 0.023 -0.014 0.000 1.00 0.00
ATOM 2 H11 MUT 1 -0.346 -0.533 0.893 1.00 0.00
ATOM 3 H12 MUT 1 -0.347 -0.532 -0.894 1.00 0.00
ATOM 4 H13 MUT 1 -0.362 1.013 0.000 1.00 0.00
ATOM 5 C2 MUT 1 1.560 -0.004 -0.001 1.00 0.00
ATOM 6 H21 MUT 1 1.951 -1.029 -0.001 1.00 0.00
ATOM 7 H22 MUT 1 1.942 0.512 0.889 1.00 0.00
ATOM 8 H23 MUT 1 1.941 0.512 -0.891 1.00 0.00
ATOM 9 O1 MUT 1 1.447 -0.012 0.003 1.00 0.00
ATOM 10 HO MUT 1 1.741 -0.940 0.000 1.00 0.00

=== ems.pdb =======================================
CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 MUT 1 15.023 14.986 15.000 0.00 0.00
ATOM 2 H11 MUT 1 14.654 14.467 15.893 0.00 0.00
ATOM 3 H12 MUT 1 14.653 14.468 14.106 0.00 0.00
ATOM 4 H13 MUT 1 14.638 16.013 15.000 0.00 0.00
ATOM 5 C2 MUT 1 16.560 14.996 14.999 0.00 0.00
ATOM 6 H21 MUT 1 16.951 13.971 14.999 0.00 0.00
ATOM 7 H22 MUT 1 16.942 15.512 15.889 0.00 0.00
ATOM 8 H23 MUT 1 16.941 15.512 14.109 0.00 0.00
ATOM 9 O1 MUT 1 16.447 14.988 15.003 0.00 0.00
ATOM 10 HO MUT 1 16.741 14.060 15.000 0.00 0.00