Dear all It is first time I am calculating free energy of protein and ligand. I am following the Justin's tutorial of methane in water free energy calculations. Though only van der waal lambda are defined so I have taken the mdp files from the alchemistry.org web page. Since the ligand and protein under my study have positive charges (one positive charge on ligand and tree positive charges on protein). So I have to add a CL ions in topology file to make a neutral sytem. Is it okay to use the system with ion for free energy calculation? If yes, What are change that can be made in mdp entry.
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