Dear all,

Currently, I am working with molecular dynamics using GROMACS. I would like to do a production run of a cyclic peptide that has an organic molecule in the center. The problem is that the ligand is detaching from the peptide at the early beginning during the energy minimization step and I would like to keep it inside.

I heard about you can define a pseudo bond between the center of mass of two molecules to prevent this phenomena in gromacs. However, I am having issues to find this in gromacs manual.

Does anybody know about that?

Thank you