[gmx-users] R-B dihedrals

[Justin Lemkul]

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

-- 
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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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