[gmx-users] two peptides in simulation tend to stick together

[MD]

Hi Gromacs folks,

I was trying a simulation to look at a protein (35kDa) and a peptide (10
amino acids)interaction. I prepped one pdb file containing both the protein
and the peptide. The original position of the peptide is in a hydrophobic
pocket of the protein from a docking result. I used 1-10 to number the
peptide and I kept the original protein numbering system (23-336) as it is,
and they are both named chain A. However after the simulation I found quite
some structures have the #10 of the peptide trying to get close to #23 of
the protein. I used the tutorial mdp file and the protein and peptide are
easy to start with (no modified residues). I wonder if I am missing some
parameters setting up at the starting point? Or by simply naming them with
different chain names will fix the problem?

Thank you in advance,

MD