On Fri, Nov 11, 2011 at 8:09 AM, Fernando Blanco <mdgamber.gmail.com> wrote:
> Thanks so much, I'm going to try
>
> Sorry, what was the function of this variable?
>
It is the 1-4 electrostatic scaling factor. The amber force fields scale
non-bonded interactions between 1-4 partners (atoms connected in a
dihedral). The non-bonded interactions for bond and angle partners are
excluded completely.
However, to increase compatibility between Amber force fields and others
that take a different approach to 1-4 scaling (i.e. GLYCAM), the non-bonded
scaling factors (SCEE and SCNB) were incorporated into the topology file so
they could be set on a per-dihedral basis (to allow for mixed scaling) and
_removed_ from the input file so using those variables would generate a
fatal error, NOT allow the user to think they were simulating with
scee/scnb really set.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 11 2011 - 10:30:03 PST
