[gmx-users] peculiar water behavior

Chetan Mahajan chetanvm10 at gmail.com
Fri Jun 13 20:45:34 CEST 2014

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)?


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
> ==================================================
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list