[gmx-users] peculiar water behavior

[Chetan Mahajan]

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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