[gmx-users] Free energy calculation of protein and ligand

[tasneem kausar]

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.

Waiting for suggestions
Thanks in Advance