[gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

[Luirink, R.A.]

Hello,
I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such).
I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions.

When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue?
Best,
Rosa