Respected Gromacs community,
I am trying to minimize a system containing 10 peptides where each peptide contains 7 amino acid residue and one ligand. I had the the residue no’s in a increasing order in the input gro file. After minimization the residue no’s of every ligand have been changed to 1. But it should be in a increasing order as it was in the input gro file. I didn’t understand why the residue no is changing and how to prevent that. If anyone can suggest a way to solve this it will be helpful.
Thanking You,
Bilash maity.