[gmx-users] R-B dihedrals
nedomacho at gmail.com
Tue Apr 14 23:27:02 CEST 2015
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.
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
>> 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 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
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