LigParGen toluene itp file

GROMACS version:2020.4
GROMACS modification: No
Hello,
I am attempting a simulation of ~ 200 toluene molecules using gmx. I used LigParGen server to create the .itp file. I used the resulting pdb file with packmol to produce a starting pdb file with 200 toluene molecules. When I attempt to minimize the structure, grompp complains that the system has a net charge and PME is not recommended.

The net charge of the system per molecule from the .itp file is -0.0001 units. However, when grompp processes the pdb file, the net charge is reported as -0.020000000 and PME is flagged as a warning. I wonder if there’s a way to work around this error. We could use coulombtype = cutoff as one alternative, however, I am curious to know if there’s a better fix? I am posting the charge section from the .itp file below.

Thank you,

; Name nrexcl
TOL 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 TOL C00 1 -0.1325 12.0110
2 opls_801 1 TOL C01 1 -0.1435 12.0110
3 opls_802 1 TOL C02 1 -0.1326 12.0110
4 opls_803 1 TOL C03 1 -0.1354 12.0110
5 opls_804 1 TOL C04 1 -0.0896 12.0110
6 opls_805 1 TOL C05 1 -0.1356 12.0110
7 opls_806 1 TOL H06 1 0.1367 1.0080
8 opls_807 1 TOL H07 1 0.1359 1.0080
9 opls_808 1 TOL H08 1 0.1366 1.0080
10 opls_809 1 TOL H09 1 0.1372 1.0080
11 opls_810 1 TOL H0A 1 0.1368 1.0080
12 opls_811 1 TOL C0B 1 -0.1907 12.0110
13 opls_812 1 TOL H0C 1 0.0922 1.0080
14 opls_813 1 TOL H0D 1 0.0922 1.0080
15 opls_814 1 TOL H0E 1 0.0922 1.0080

-0.0001 is too small, u can just round it off to zero.

Not when the charges are actually reported to four decimal points. It is clear that this is an actual deficiency because the charges sum to -0.0001 when they should not. The charge in the ligand topology needs to be adjusted so it sums to 0. The accumulation of this error when there are 200 molecules of this type (-0.02) is definitely non-negligible.