[gmx-users] peculiar water behavior

[Chetan Mahajan]

The pics should be seen in the reverse order. Due to sorting by name,
"After equilibration" pic occurs first.


On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan <chetanvm10 at gmail.com>
wrote:

> Thanks.
>
> No, same things do not happen when it's a NVT simulation or no mixed
> potentials. Also, with mixed potentials in NPT simulation, this things of
> slab moving in one direction (thus following water movement) happens only
> with -com option of refcoord-scaling, *not with -all option for
> refcoord-scaling. *
>
> I have a crystal slab with equal amount of water on both the sides. During
> NPT equilibration (with refcoord-scaling option of -com, not -all), some
> water on side side of the slab enters opposite side due to periodic
> boundary conditions I have (say water on the right side of the slab,
> crosses boundary of the box and enter the left side of the slab due to
> periodic boundaries. Even crystal slab follows this water and move same
> distance in the same direction of water movement. Following link shares
> pictures of the solvated slab before and after equilibration:
>
>
> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
>
> I feel, this is not an error, but it is odd. Due to periodicity we have,
> output of any calculations will remain the same.  Again, with -all option
> for refcoord scaling, this movement of water and slab DOES NOT occur.
>
> Thanks a lot!
> regards
> Chetan
>
>
> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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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