[gmx-users] peculiar water behavior

Chetan Mahajan chetanvm10 at gmail.com
Sat Jun 14 03:28:45 CEST 2014

Other main observation is that crystal slab following water, moving in the
same direction, *despite of position restraints (refcoord-scaling=com
option). *

On Fri, Jun 13, 2014 at 1:45 PM, Chetan Mahajan <chetanvm10 at gmail.com>

> 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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