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

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 30 18:29:08 CET 2014

On Thu, Oct 30, 2014 at 2:39 PM, Turgay Cakmak <turgaycakmak34 at gmail.com>

> 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?

No, there is no double-counting.

> In other
> words, is it always true that <total vdW interactions = LJ(14) + LJ (SR)>
> (please assume that long-range interactions are negligible).

Well, yes, but since the values of parameters are all coupled through the
parameterization process, there isn't a true correspondence... 1-4
parameters are scaled in some force fields precisely because some component
of those interactions is already described by dihedrals...

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

Same applies.

> 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?

Potentials are scalar, forces are directional, magnitudes of forces are
scalar. Be precise about what you mean, and the correct operation becomes
clear :-)


For the record, I am simulating a fiber composed of several hundred peptide
> molecules.
> Thank you for your time.
> Turgay
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