Greetings The discussion list had helped me about understanding what to do when I want to calculate binding free energy using LIE after doing MD simulation using PME. Now I need your help about choosing the simulation box size for ligand and complex. I used -d 1.0 in editconf for the complex simulation and -d 1.6 for the ligand simulation. Are this values ok? Should I use a different value of -d for the ligand simulation? Thank you Williams
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