System has non-zero total charge

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Dear Gmx Users,
I am dealing with a 380k atoms system whose net charge is not “strictly” zero.
During the grompp generation, indeed, gromacs detects a net charge equal to -0.018.
I do believe this is a numerical problem, do you think it is correct to use the option maxwarn -1 in order to ignore the warning and go ahed running the simulation?

Thanks in advance

Luca

2

Hi,
It looks a little too large to be a rounding error. You can check the topology by looking at the right-hand comment column of the atom listing (in the topology), which lists the cumulative charge. This should be an integer after every residue (and/or charge group where applicable). This will assist in finding the residue where things start departing from integer values. Also check the terminal capping groups that have been used.

Best regards
Alessandra