[gmx-users] Should I restrain omega dihedrals or just phi/psi?
jalemkul at vt.edu
Wed Dec 21 03:21:07 CET 2016
On 12/20/16 8:08 AM, Daniel Bauer wrote:
> 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 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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