[gmx-users] crystal slab and position restraints: com option

Justin Lemkul jalemkul at vt.edu
Mon May 12 14:00:10 CEST 2014

On 5/11/14, 2:01 PM, Chetan Mahajan wrote:
> Thanks, Justin. I was also under impression that with "com" option,
> distance between slab atoms (which are position restrained) remains same,
> even though coordinates change. So doesn't it mean that TiO2 slab
> dimensions should remain same?

No.  Under NPT, the box will change.  That's the point of pressure coupling. 
Bonds that are constrained will stay constrained, but other interatomic 
distances can vary according to the scaling factor introduced by the barostat. 
In the case of "refcoord_scaling = com," each atom's position is scaled relative 
to the COM of the reference coordinates, not the absolute coordinates of each 
atom (as would be the case when using "refcoord_scaling = all").



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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