How to Extract RMSD of Peptide-Protein Interaction Without Mixing Atoms in GROMACS?

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GROMACS version: 2022.3-plumed_2.8.1
GROMACS modification: No

Hello everyone,

I am working on a peptide-protein interaction simulation and I want to extract the RMSD of the interaction as suggested by mdtutorials. Specifically, I need to calculate the RMSD of the heavy atoms of the ligand (peptide) and the backbone of the receptor (protein).

However, when using the “Backbone” selection in GROMACS, it mixes the information from both the peptide and the protein, which is not what I want. I already created an index file where I separated the peptide and protein into different groups, but the problem is that these groups include all atoms from each of the two components, not just the backbone for the receptor and the heavy atoms for the ligand.

How can I modify my index file or selection to only include:

  • The heavy atoms of the peptide (ligand)
  • The backbone atoms of the receptor (protein)

Any suggestions or guidance on how to separate these selections properly for RMSD calculation would be greatly appreciated!

Thanks in advance!