Calculating distance between centroid of aromatic rings using center of geometry

[alevilla]

Hi,
gmx distance is not the appropriate tools to use. gmx pairdist may be more appropriate. See this post for the difference

What is the difference between gmx distance, gmx mindist and gmx pairdist?

Hi, I am trying to compute distance between four residues of a protein involved in active site. I am getting confused in mindist, pairdist and gmx distance. What are the limits and differences in three? Which analysis can be helpful in plotting distance between A-B, B-C, C-D and D-A residues over time, where ABCD are 4 residues forming bottleneck for ligand entry.

\Alessandra