The GROMACS official documentation (see here) states that a system with non-zero total charge will yield an error:
System has non-zero total charge
Notifies you that counter-ions may be required for the system to neutralize the charge or there may be problems with the topology.
If the charge is a non-integer, then this indicates that there is a problem with the topology. If pdb2gmx has been used, then look at the right hand comment column of the atom listing, 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 capping groups that have been used.
If the charge is already close to an integer, then the difference is caused by rounding errors and not a major problem.
Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. Nevertheless, it is standard practice to actually add counter-ions to make the system net neutral.
If I understand this correctly, it means that a uniform background charge will be added to a net-charged system. What if I wanted to study a charged system, e.g. a peptide with basic groups in the gas phase, where counter ions are absent. Is it still possible to perform a gromacs calculation on such a system and how will the introduction of the compensating background charge affect the molecular dynamics?
I then looked into other packages and noted that net-charged systems seem to be generally problematic in mm calculations. Can anyone point me into a direction like literature on this?