No, this does not happen at the parameter level. It's done inside the code,
based on flags in the prmtop that say whether a given 1-4 pair (defined
from the torsion list) should be scaled. The actual parameters in the
prmtop are not scaled. The scaling factor is discussed in the original
Cornell et al ff94 paper that set the values used by most current amber
protein force fields.
On Mon, Oct 7, 2019, 8:45 PM Nate Guerin <nguerin.cs.duke.edu> wrote:
> Hello,
>
> I am reading the Amber 18 manual and noticed in section 14.1.6 the
> sentences:
>
> “By default, vdW 1-4 interactions are divided (scaled down) by a factor of
> 2.0, electrostatic 1-4 terms by a
> factor of 1.2. These are default values for the protein force fields and
> GAFF, but not for sugar force fields GLYCAM_
> 06EP and GLYCAM_06, for example, in which these interactions are not
> scaled at all.”
>
> Does this mean that in the parameter files, e.g. ff14SB, the R_{i,j} are
> scaled down by a factor of two, or rather that the contribution to the
> contribution that the van der Waals terms contributes to E_{total}
> (equation 14.1) is scaled down by 2. And if the latter, why?
>
> Thank you!
>
> Nathan Guerin
> PhD Student
> Donald Lab – Duke University
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 07 2019 - 18:30:01 PDT
