Membrane Protein Ligand Complex Simulation Inquiry?

Hello to perform a simulation of a ligand-transmembrane protein complex embedded in a membrane would the best methodology be to first simulate the ligand membrane protein complex separately and then simulate it once more embedded in the membrane or just the later?

Kind Regards,

It doesn’t make sense to simulate an integral membrane protein in water without the membrane. The structure is incompatible with being exposed to water and will likely distort.

Hello and thank you for your kind update and ok, I wanted to confirm that the ligand can be included in the membrane simulation.