To what extent can the electrostatic interactions as returned by gmx energy be interpreted as having any physical meaning? My understanding from the protein-ligand tutorial is that the coulombic and lennard-jones interaction energies are only meaningful when summed into a total interaction energy, and also that extracting individual energies of various components has no physical meaning.
So I just wanted to check, would it make sense to extract the total interaction energy between residues of the same molecule and compare their relative values between different conformations of the molecule, or does it only make sense to do so for 2 separate molecules?