Gromacs version : 2019
My system is a polystyrene melt and I want to calculate RDF between center of mass of inter-chain benzene rings.
I made a index containing atom numbers of the rings. and used the command:
gmx rdf -f traj_comp.xtc -s ps.tpr -n ps.ndx -selrpos mol_com -seltype mol_com -o rdf.xvg
But I have a confusion, is it calculating RDF between COM of each benzene with other (by taking COM of 6 atoms of ring), or it will just take whole group (containing atom no. of all benzenes) as one and not individual rings.
How can I approach this?