I usually add counter ions (Na or Cl) to neutralize system during dynamics but if a protein is already in neutral condition with a condition "No ions to add and no potential to calculate", what is the right method to over come it?
That just means your system already has a zero net charge.
Note that counterions alone are usually insufficient to adequately model biomolecular systems, and an additional 100-150 mM of salt is typically added to the simulation box to better model most experimental or in vivo conditions.
@justin - Thank you sir. When you mean "SALT" do you mean that, i should both Na & Cl? Is that possible in gromacs? Could you please help me more about it?
You should use whatever salt makes sense for the system you're trying to model.
Use the -conc -pname -nname options as needed.
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