Total charge error in .itp files

User discussions
1

I’m trying to run MD on my system with hexane but I keep receiving this error. I have noticed that my .itp files do have this net charge on my structure (generated through Avogadro then converted into .itp and .gro with http://zarbi.chem.yale.edu/ligpargen/). Is there any way I can generate an .itp with the right net chat (that should be zero)? Or perhaps some way to teach Gromacs to round this number? The program runs the simulation with this net charge, but once I’m introducing about a thousand molecules it crashes.

“NOTE 2 [file topo.top, line 11]:
System has non-zero total charge: 0.000100
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.”

GROMACS version: 2018.1
GROMACS modification: Yes/No
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2

Someone else reported almost an identical problem just a few days ago (please search the forum), you should verify if the topology itself has a net charge by summing the partial charges yourself. If it does, you will need to correct it. The LigParGen server has produced such output before. Any imbalance should be obvious in a molecule as simple as hexane, which is symmetric and should actually already exist within OPLS.