Smeared Charge System

When using PME with a net charged system, GROMACS applies a background charge to neutralize the system. This is not physical and not as realistic as adding counter ions. But the effect should be similar to smearing the counter charge over the atoms in the system.

A neutralizing background charge, or smearing the counter charge may not be the solution. See, e.g., [gmx-users] What's the point of adding ions to neutralize the system? and Electroneutrality in the MD Simulation for some more information.