I have a ligand located inside protein which is embedded into lipid bilayer in water environment (system = ligand + protein + membrane + water and ions). I would like to calculate energy of the ligand to protein. I have done 1 complete cycle with with couple-moltype = ligand. What should i could do next ?
If you're doing a free energy cycle with the decoupling approach in Gromacs, that is not FEP. You can easily evaluate the free energy change using the built-in g_bar program. See, for instance, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
If you want to calculate binding free energy, you need to also do a free energy cycle of the ligand in water, and take the difference of DGcomplex and DGsolv.
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