[gmx-users] peculiar water behavior

[Mark Abraham]

Hi,

Repeating myself - simplify things! Do sane things happen with NVT? With no
mixed potentials?

Your words aren't making sense to me - you'll do much better with pictures,
making sure you turn on your visualizer's option to show the periodic box.

Mark


On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan <chetanvm10 at gmail.com>
wrote:

> Hi Justin,
>
> I, actually, do not want to preserve any voids. Initial void that I
> mentioned is supposed to be filled by water during equilibration and it
> does so. However, problem is that some or major quantity of water moves out
> from one side of the box to enter from the opposite side (obeying periodic
> boundary conditions) and crystal slab moving following water movement. Thus
> although initially there is almost equal amount of water on both sides of
> the slab, we have more water on one side of the slab than the other side
> after equilibration. In other words, length of the box on one side of the
> slab is more than the other side after equilibration, although it is same
> on both sides before equilibration. My dilemma is whether this is due to
> pressure coupling or any gromacs thing or due to potentials (mixed
> buckingham and LJ)?
>
> Thanks
> Chetan
>
>
> On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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
> >
> > --
> > ==================================================
> >
> > 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
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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