GROMACS version:
GROMACS modification: Yes/No
I have a question about AB-FEP for protein-ligand in water. For the thermodynamics cycle, there are two main deltaG: 1) Protein-ligand ↔ Protin-Dummy (delta G3), 2) Ligand in Water ↔ Dummy in Water (delta G1).
Binding free energy is delta G3 - delta G1.
This is my question. To calculate delta G3 (protein-ligand), do I have to simulate only protein-ligand without water?
Thank you.
Best regards,
Chang