[AMBER] Question about ff14SB and parameter files

From: Nate Guerin <nguerin.cs.duke.edu>
Date: Mon, 7 Oct 2019 20:45:40 -0400


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

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Received on Mon Oct 07 2019 - 18:00:01 PDT
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