GROMACS version:
GROMACS modification: Yes/No
Hello all,
I am new to gromacs, i have a few confusions regarding protein-ligand simulations
“When performing MD simulations on a protein-ligand complex involving a cofactor and a substrate, is it necessary to include the cofactor in each simulation for different substrates? Additionally, how can I effectively isolate and analyze the dynamics of the protein in complex with only one ligand (substrate), excluding the cofactor from the resulting trajectories?”
I request you to clarify the question… Thank you