[gmx-users] R-B dihedrals

[Mark Abraham]

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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