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

[Mark Abraham]

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

> 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 :-)

Mark

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