Gmx-mdmat-queries

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GROMACS version: 2023.1
GROMACS modification: No
I performed a simulation of a system containing protein, tRNA, ligand, magnesium ion, sodium ions, chloride ions, and water molecules. I calculated the ratio of the number of contacts for tRNA using the command:

gmx_mpi mdmat -f md-last500ns.xtc -s md_0_1.tpr -n RNA.ndx -no num_contacts-RNA.xvg

The residue-wise values of RMSF and the ratio of contacts showed similar behavior.
I would like to know how

  1. Is this ratio calculated?
  2. How are total and mean contacts calculated for the ratio?
  3. The total contact includes intramolecular or intermolecular or all contacts within a cutoff of 1.5 nm?
  4. It’s quite difficult to get any document stating the formula used or the algorithm followed in this calculation to understand how these values are actually calculated.
    It would be great if you could provide some insights.
    Thank you in advance.
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