GROMACS version: 2021.3
GROMACS modification: No
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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
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
The contents of the itp file are:
[ 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:
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