[gmx-users] SR and 14 terms for LJ and Coulomb interactions

[Turgay Cakmak]

Dear Gromacs Users,

Thank you for your insightful comments. I am, however, still a bit confused
about the non-bonded terms in potential energy, so I would be happy if you
assisted me for a bit further.

Is there any possible overlap between SR and 1-4 interactions? In other
words, is it always true that <total vdW interactions = LJ(14) + LJ (SR)>
(please assume that long-range interactions are negligible).

Similarly, does <total Coulombic interactions = Coul(14) + Coul(SR)> hold
in all possible cases?

In addition, vdW and Coulombic interactions are directional. Is a vector
addition necessary to get the total strength of these interactions, or does
only adding up the scalar values yield an accurate sum?

For the record, I am simulating a fiber composed of several hundred peptide
molecules.

Thank you for your time.

Turgay