The charge problem of the system

Dear all:
When I apply coul/long to the System, the log file prints the warning “System is not charge neutral, net charge = 4352”, but the number of atoms with positive and negative charges in the data file is equal. I would like to ask why this happened?


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Most likely the charge you are giving each atom type is not the same, something like +1 vs -0.47.

What you show and what you say is contradictory. You say the sum of the atom charges in the data file is zero. But what you show us are commands for the input file. Without seeing the data file and the complete input we cannot say for certain that the charges compensate. There could be atoms with charges that your group/set commands don’t cover.

No. You are NOT paying attention. Since you only reset the charges for some atoms in the input with the set commands, anything is possible from what you import in the data file. So theoretically is is quite possible to have a non-neutral system. What if you add a line set group all charge 0 before the two other set ... charge commands?