[gmx-users] peculiar water behavior

Justin Lemkul jalemkul at vt.edu
Fri Jun 13 14:45:09 CEST 2014

On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
> Dear All,
> I am simulating TiO2 crystal solvated by water  and ions like sodium and
> formate. I am observing one peculiar thing, and I would like to rectify
> that. I have initial structure of crystal slab at the center of the box
> elongated in z-direction and almost equal boxlength on both the sides, with
> a gap of 1 nm between slab surface and first layer of water close to slab.
>   This space is kept to avoid water going on the sides of the crystal during
> equilibration. This was a minor information. Now, the main observation is
> that during NPT equilibration, water from one side of the slab enters the
> other opposite side of the slab (using periodic conditions) so that
> boxlengths on both sides of the slab are very different at the end of
> equilibration. Is this an artifact of pressure coupling? Following is my
> equilibration .mdp file. I have tried varying the compressibility and tau-p
> parameters in the following file. e.g. zero compressibility in x/y
> direction or tau-p reduced to 3.

With pressure coupling, any voids present in the system will be compressed.  If 
you need to try to preserve some sort of vacuum layers, use NVT.



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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