GROMACS version: 2023.3
GROMACS modification: No
I have protein-protein complex, where one protein is a ligand and other is a receptor. Is it necessary to use -merge (ON or AUTO) option when topology is created with pdb2gmx complex? Would it better to merge chains into one molecule type in topology or not, in order to get more accurate results in mdrun for such protein-protein complex?
It is better to keep separate chain, you need to identify the protein and ligand for analysis.
Thank you