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

Justin Lemkul jalemkul at vt.edu
Sun May 11 19:57:33 CEST 2014

On 5/11/14, 1:51 PM, Chetan Mahajan wrote:
> Dear All,
> I am new to GROMACS. I am simulating TiO2 crystal slab (2160 atoms, slab
> dimensions:  30.63 A0 x 37.76 A0 x 21.05 A0) solvated by 3656 water
> molecules, 1 sodium ion and 1 formate ion. I am applying position
> restraints to each Ti and O with refcoord-scaling: com. With com option, we
> expect crystal to not change in dimensions, but my crystal slab dimensions
> after equilibrium and production runs are 29.82 A0 x 35.91 A0 x 19.52 A0.
> So we see that slab has shrinked. Is this okay?

Using NPT, the box dimensions will change.  The "refcoord-scaling = com" option 
means the resulting positions are scaled based on the COM of their reference 
positions.  None of those conditions would suggest the box or coordinates won't 



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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