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

[Luirink, R.A.]

What I have tried is, instead of adding them to the [ pairs ] block, is change the epsilon value manually via the [ nonbon_params ] block. However, I can’t manually change the electrostatic interactions to account for the fudgeQQ (0.8333) for these specific pairs (or at least, I haven’t found a way to do so).


From: "Luirink, R.A." <r.a.luirink at vu.nl>
Date: Thursday, 6 February 2020 at 11:49
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

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