[gmx-users] how to extract the LJ interaction parameters from the tpr file

[Baofu Qiao]

Hi all,

I want to calculate the non-bonded interactions (LJ+Coulomb) between two
sub-groups when they are within the cutoff distance. The sub-groups are
only parts of the whole energy groups used in my .mdp file. Given the
partial charges of the atoms involved are easy to get from the 
"top.atoms.atom[index[i]].q",   I have no idea how to get the LJ
parameters of the atoms?

Does anyone know how to get them from the top.atoms.atomXXX? Or is there
some similar code to calculate such energies?

Thanks in advances!
Best wishes,
Baofu Qiao