[gmx-users] Nonsymetric molecule across pbc

Justin Lemkul jalemkul at vt.edu
Tue Feb 18 18:03:50 CET 2014

On 2/18/14, 11:19 AM, Steven Neumann wrote:
> Dear User,
> Can you please write me how to build a system of a protein (nonsymetric
> obviously) and place it in the on the box edge so that one half is within
> the unit cell and another one is copied across pbc on the other side? I
> assume I will get the error doing manually...

Assuming box vectors of length x, y, z:

editconf -center x/2 y/2 z

will split the molecule across the boundary in the positive z-dimension.

I can't think of a situation where this serves any useful purpose that centering 
does not, but that's how you'd do it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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