Hello, I am facing a problem while trying to neutralize my molecule. My molecule is a protein and after writing input file[.tpr] on seeing a charge of 6.00000e+ i am trying to neutralize it by using 6 CL- ions. when i have tried 'genion' for small molecules it was running fine,but for this molecule it has been running since 2 days. The only message being shown is that only 1 CL- has been introduced.Can you please help me out with the necessary steps needed. I am actually new to Gromacs,so please help me get through and if possible suggest some good material.
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