RDF between center of mass of benzene rings

User discussions
1

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?
Thanks

2

Hi,

gmx rdf -f traj_comp.xtc -s ps.tpr -n ps.ndx -selrpos mol_com -seltype mol_com -o rdf.xvg

is calculating the RDF between COMs of each benzene molecule. You should get a first pick at around 0.55/0.6 nm.
Kind regards
Alessandra

3

It really depends how you have the residues named within the and how you are selecting the groups.
Set the exclusions for the polymer molecule topology such that it covers the entire length of the molecule.