Hi Dave,
This is a question about the latter. Because GLYCAM uses no scaling factor
(or scaling factors of 1) for dihedrals and the standard Amber force fields
use 1.2 (EEL) and 2.0 (VDW), we need a way of specifying different scaling
factors for different dihedrals so that both force fields work together the
way they were parametrized to.
To address this, amber11 introduced 2 new sections into the prmtop files:
FLAG ONE_SCEE and FLAG ONE_SCNB (I've updated the prmtop documentation at
http://ambermd.org/formats.html to reflect this). These are actually
1/scaling factor. Sander and pmemd simply use these dihedral-specific
scaling factors for each dihedral term they calculate instead of some global
one set in the mdin file.
If, on the other hand, the prmtop does not have ONE_SCNB or ONE_SCEE present
in the prmtop file, it just uses the amber defaults 1.2 and 2.0.
If you can simply emulate this behavior, that would be great. Only sleap
can write these files, but they're indexed in exactly the same way as the
dihedral force constants, etc. I don't recall how multi-term dihedrals were
treated, but I think only the first scaling factor was used (since they
should all be identical). You don't want to scale it multiple times,
though.
Hope this helps,
Jason
On Wed, Apr 6, 2011 at 9:58 AM, <dcerutti.rci.rutgers.edu> wrote:
> If this is a question about being able to tune to factor that scales 1:4
> interactions (5/6 for vdW, 1/2 for electrostatics in the AMBER force
> fields) then the answer for mdgx is "yes." From the beginning, this factor
> has been specifiable by the user. However, if you're referring to some
> form of pair-specific scaling that places different factors for different
> dihedral interactions, the answer is "no." Wouldn't be too hard to
> implement, though, if that is something that people really want to
> explore...
>
> Dave
>
> > On Tue, Apr 05, 2011, Jason Swails wrote:
> >>
> >> Just a quick question -- does NAB have the variable 1-4 scaling added to
> >> sander/pmemd?
> >
> > I'm pretty sure the answer is "no"; same question is now appropriate for
> > mdgx
> > as well....sigh
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 06 2011 - 10:30:03 PDT
