# WARNING: Listed nonbonded interaction between particles larger than the table limit **URL:** \ **Category:** User discussions\ **Created:** [March 27, 2023, 1:46pm UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053 "2023-03-27T13:46:26Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [March 27, 2023, 1:46pm UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053/1 "2023-03-27T13:46:26Z")
GROMACS version: 2021.3 GROMACS modification: No Here post your question I am simulating aggregation of polymer chains on a surface in acetone as solvent. When I simulate the polymers in solution (without the surface), the simulation runs fine for 100 ns. However, when I introduce the surface, the energy minimization and NVT equil steps run fine. However, the NPT production run fails with the error ```auto WARNING: Listed nonbonded interaction between particles 46272 and 46281 at distance 4.662 which is larger than the table limit 2.302 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. step 99800, will finish Mon Mar 27 20:38:59 2023Segmentation fault (core dumped) ``` The atoms in question are the oxygen and hydrogen atoms (acetone has a formula CH3-CO-CH3). I tried creating the system from scratch multiple times but the error keeps on popping up in the production run; the solvent molecule giving the error changes but everytime the error is between the oxygen atom and one of the hydrogens in acetone. As a hack, I tried deleting the molecule throwing the error but after a few steps another acetone molecule will spit the same error. The topology was obtained from CHARMM-GUI server and is apparently correct since the polymer solution simulations work fine. The itp file is also similar to what others have also used e.g., at [https://gitlab.com/MiMiC-projects/MiMiC-docs/-/archive/main/MiMiC-docs-main.tar.gz?path=docs/tutorials/AcetoneTutorial](https://gitlab.com/MiMiC-projects/MiMiC-docs/-/archive/main/MiMiC-docs-main.tar.gz?path=docs/tutorials/AcetoneTutorial) The contents of the itp file are: ```auto [moleculetype] ; name nrexcl ACTO 3 [atoms] ; nr type resnr residu atom cgnr charge mass 1 OG2D3 1 ACTO O1 1 -0.480000 15.9994 ; qtot -0.480 2 CG2O5 1 ACTO C1 2 0.400000 12.0110 ; qtot -0.080 3 CG331 1 ACTO C2 3 -0.230000 12.0110 ; qtot -0.310 4 CG331 1 ACTO C3 4 -0.230000 12.0110 ; qtot -0.540 5 HGA3 1 ACTO H21 5 0.090000 1.0080 ; qtot -0.450 6 HGA3 1 ACTO H22 6 0.090000 1.0080 ; qtot -0.360 7 HGA3 1 ACTO H23 7 0.090000 1.0080 ; qtot -0.270 8 HGA3 1 ACTO H31 8 0.090000 1.0080 ; qtot -0.180 9 HGA3 1 ACTO H32 9 0.090000 1.0080 ; qtot -0.090 10 HGA3 1 ACTO H33 10 0.090000 1.0080 ; qtot -0.000 [bonds] ; ai aj funct b0 Kb 1 2 1 2 3 1 2 4 1 3 5 1 3 6 1 3 7 1 4 8 1 4 9 1 4 10 1 [pairs] ; ai aj funct c6 c12 or ; ai aj funct fudgeQQ q1 q2 c6 c12 1 5 1 1 6 1 1 7 1 1 8 1 1 9 1 1 10 1 3 8 1 3 9 1 3 10 1 4 5 1 4 6 1 4 7 1 [angles] ; ai aj ak funct th0 cth S0 Kub 1 2 3 5 1 2 4 5 3 2 4 5 2 3 5 5 2 3 6 5 2 3 7 5 5 3 6 5 5 3 7 5 6 3 7 5 2 4 8 5 2 4 9 5 2 4 10 5 8 4 9 5 8 4 10 5 9 4 10 5 [dihedrals] ; ai aj ak al funct phi0 cp mult 1 2 3 5 9 1 2 3 6 9 1 2 3 7 9 4 2 3 5 9 4 2 3 6 9 4 2 3 7 9 1 2 4 8 9 1 2 4 9 9 1 2 4 10 9 3 2 4 8 9 3 2 4 9 9 3 2 4 10 9 [dihedrals] ; ai aj ak al funct q0 cq 2 3 4 1 2 ``` I searched in the mailing list and found that this error arises during free energy simulations. However, I am not performing any free energy calculations. The production mdp is as follows: ```auto define = -DPOSRES_S -DPOSRES_SURF=1000.0 integrator = md dt = 0.002 nsteps = 5000000 nstxtcout = 50000 nstvout = 50000 nstfout = 50000 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 rlist = 1.2 rcoulomb = 1.2 coulombtype = PME ; tcoupl = v-rescale tc_grps = SYSTEM tau_t = 1.0 ref_t = 298 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 12.0 compressibility = 4.5e-5 ref_p = 1.0 constraints = none continuation = yes nstcomm = 100 refcoord_scaling = all ``` Can anyone please help me resolve the issue. Thamks, Raman ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [March 27, 2023, 3:55pm UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053/2 "2023-03-27T15:55:49Z")
The surface is the problem, not the acetone. Note how things worked until you added the surface. What is the surface, is it some kind of infinite grid of atoms? Do you need `infinite-molecules` to be set in the `.mdp` file? ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [March 27, 2023, 4:50pm UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053/3 "2023-03-27T16:50:00Z")
Hi Justin, Thanks for the reply. The surface is an arc of cylinder cut out from a very large diameter carbon nanotube. It is not an infinite or periodic molecule but is finite sized. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [March 28, 2023, 3:30am UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053/4 "2023-03-28T03:30:52Z")
Are the edges properly capped with H atoms? Are there atoms right at the box boundary such that they clash across periodic boundaries? When extracting a subset of atoms from something that was originally a different shape, you’ll often run into trouble like this. ---
**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\ **Post date:** [March 29, 2023, 11:28am UTC](https://gromacs.bioexcel.eu/t/warning-listed-nonbonded-interaction-between-particles-larger-than-the-table-limit/6053/5 "2023-03-29T11:28:55Z")
Hi Justin, I double checked the structure and gro files. The edges are hydrogen capped and all valencies are satisfied. The minimum distance between the box edge and the nearest atom is \>1 nm so I guess this is not an issue. Increasing this distance to 1.5 nm and then solvating with acetone did not solve the problem. Interestingly, if I skip the NVT equil and directly jump to NPT using Berendsen barostat, the simulation runs fine for atleast 10 ns. But Berendsen not being a preferred barostat can not be the way ahead (that’s my understanding of Berendsen). A short equil with Berendsen and then production run with P-R also fails with same error. When I use TIP3P water as solvent instead of acetone, the simulation smoothly runs through minimisation, equil and 50 ns prod runs without any problem. I am using CHARMM36 FF. Thanks for looking into this. Raman