# Fatal error, depending on absolute position **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [December 8, 2021, 9:00pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-depending-on-absolute-position/3271 "2021-12-08T21:00:56Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![michael.brunsteiner](https://avatars.discourse-cdn.com/v4/letter/m/7cd45c/32.png) [@michael.brunsteiner](https://gromacs.bioexcel.eu/u/michael.brunsteiner)\ **Post date:** [December 8, 2021, 9:00pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-depending-on-absolute-position/3271/1 "2021-12-08T21:00:56Z")
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