Hi,
As far as I understood, you have a protein and ligand (not covalently
bonded) and you want to switch off the interaction
between one aminoacid and the ligand.
Concerning approach 1,
If you have a merged topology (only one topology file with one [molecular
type] in your case protein and ligan
Dear GROMACS users,
I am new to GROMACS software and have a question about switching off
pair-wise non-bonded interactions between two molecules.
I have a simulation box composed of a protein with a substrate inside the
protein catalytic pocket and there are no covalent bonds between protein
amino
