[gmx-users] crystal slab and position restraints: com option
chetanvm10 at gmail.com
Sun May 11 20:01:40 CEST 2014
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?
Thanks a lot
On Sun, May 11, 2014 at 12:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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,
>> 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 change.
> 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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