Calculation of free energy surface

User discussions
#1

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) ?

#2

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

#3

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