I suggest starting with the LAMMPS water example in examples/gcmc and then add your protein to it. Once that is working, add your graphene sheet to the water example. Finally combine water, protein,and graphene sheet in a single simulation. It is not obvious to me that such a simulation is scientifically useful. You would probably be better off changing the chemical potential of water by running NVT dynamics at different volumes, or maybe NPT at different pressures.
Aidan
Thank you so much for your suggestion. I just do not understand this sentence
“You would probably be better off changing the chemical potential of water by running NVT dynamics at different volumes, or maybe NPT at different pressures.”
Could you please explain it a bit more. Why is it useful?