First, docking was performed after deletion a protein subunit.

Gromacs (latest version and forcefield used )used for the simulation.

we have experimental validation of active site and the potency of compound but we are getting the proper data.

Actually the literature behind the study was interesting, a transmembrane complex was about to item of our study. But we can not replicate the lipid membrane in complex with a ligand.

Please suggest me, how do I perform membrane simulation with protien-ligand complex in gromacs. or without lipid membrane how can I validate the results.