[gmx-users] R-B dihedrals

[Alex]

Mark, we just figured it out, thanks. :) And yes, you are definitely onto
something: two identical dihedrals pulling in opposite directions. This is
what happens when people from solid state show up to use GMX. :)

Alex

On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Can you shift it to 40 degrees?
>
> Mark
>
> On Tue, Apr 14, 2015 at 11:26 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima
> at
> > 45 and 315 and a peak around 180. Checked if I converted to R-B
> > coefficients correctly -- same thing. At 90/270 clean decrease to 45/315.
> >
> > Alex
> >
> >
> > On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 4/14/15 5:12 PM, Alex wrote:
> > >
> > >> Tried both, the (now enormous) parameters are read in correctly,
> nothing
> > >> in
> > >> output mdp that catches my eye. No constraints used in the system,
> > >> explicitly set in mdp. Plotted the potential at 45/315 deg minimum --
> > >> definitely nonzero at 90 degrees (starting config). This has got to be
> > the
> > >> strangest GMX issue i've ever had.
> > >>
> > >>
> > > What does a 1-D energy surface look like for that dihedral?  You've
> got a
> > > dihedral at 90 in the coordinates and you're trying to shift it to 45?
> > If
> > > there's a massive barrier in between, EM won't necessarily do that for
> > you.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > >
> > > --
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