Calculation of free energy surface

GROMACS version: 2020.4

I want to plot the free energy surface diagram by using Rgy and rmsd data but what should i select among many choices (backbone,c-alpha mainchain-cbeta, system) ?

What makes the most sense for your system? What value will characterize the type(s) of structural changes you are seeing?

For polymer transition, the backbone should be selected. See this paper for more info.