I am trying to simulate a system having some cations, anions, and neutral solvent (Ethylene Carbonate) molecules. While I am trying to maintain the charge of the system by taking 5 anions (each having charge -1) and 5 cations (each having charge +1) system with neutral solvent (zero charges of Ethylene Carbonate), I suppose to get a neutral charge for the overall system. But I am getting a non-zero charge during the minimization time (approx -0.2237), for this reason, I couldn’t able to proceed my simulation. There is no problem with the cations and anions because in a separate simulation I was taken 5 cations and 5 anions and I got a zero charge of the system but when I added the neutral ethylene carbonate to the system the above problem I faced.
Can you please help me in this regard or else suggest to me how to proceed with my simulation?
Such a fractional charge likely means your ethylene carbonate topology is incorrect. Were you warned about a net charge when compiling the .tpr file for use with genion? If not, it is also possible that you made an inappropriate choice in which group to replace with ions, leaving fragmented molecules behind.