Hi Roshan,

I'm not exactly sure how to do this in Gromacs with mdmat, but I imagine there's a workaround based on how you create the index file. For instance, you could make your index file only C-alphas of residues as an approximation of center of mass for all residues, or index selections of whole domains if that's what you're interested in.

Gromacs utilities are great but often don't lend themselves to the easiest customization.

To do a more advanced analysis I would recommend checking out MDAnalysis, specifically the contact map functionalities:

https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/contacts.html

Good luck!

Thanks Kyle. I wanted to find the interacting residues through contact map, but the plot from gmx mdmat is terribly hard to comprehend. I created two separate index for all the atoms of peptide 1 and then peptide 2 and throw it into gmx mdmat, but I am not getting any interacting residues at all since it just looks like contact map for self interacting peptide.

1.ps is the contact plot I got from VMD's contact map plugin while the another one is from gmx mdmat