[gmx-users] How to obtaine different protein orientations in a biphasic system

[Justin Lemkul]

On 11/12/14 3:29 PM, James Lord wrote:
> Dear users,
> I have inserted a protein in a biphasic system (like Justin tutorial). My
> question is if I want to sample different orientations of protein to one of
> the phases how should I do that? I have rotated the protein with different
> angles  (90,180,270) around X,Y,Z axes  but as I have periodic boundary
> condition in XYZ, Am I really obtaining different orientations? any
> comments is appreciated

The only rotations that yield equivalent orientations are the ones in the plane 
of the interface, i.e. if the interface is along x-y, then rotating around z 
does nothing.  The other rotations indicate different initial configurations 
relative to the interface.

-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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