[gmx-users] Should I restrain omega dihedrals or just phi/psi?

[Justin Lemkul]

On 12/20/16 8:08 AM, Daniel Bauer wrote:
> Hello,
>
> Im working on MD simulations of membrane proteins and want to restrain the
> backbone dihedrals of some amino acids. I now wonder if its sufficient to
> restrain only phi/psi dihedrals as shown in the manual (
> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints), or if I
> should also set restrains on omega dihedrals?
>

Restraining omega will keep the peptide bonds from cis-trans isomerization, 
which is exceedingly rare under normal ambient conditions with most force 
fields; I don't see what restraining it would do.  If you want to preserve 
secondary structure elements, restrain phi and psi.

-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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