[gmx-users] Location of Bubbles.

[sujithkakkat .]

Thank you Mark and Jan.

On Sat, Jul 18, 2015 at 3:59 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If your box is periodic then there are no edges or faces... Also note that
> if you mentally divide your box in e.g. three parts in each dimension, the
> 27 resulting cubes have 26 that are near an original edge or face, so of
> course things will look like they happen near edges and faces...
>
> Mark
>
> On Sat, 18 Jul 2015 09:49 Jan Jirsák <janjirsak at gmail.com> wrote:
>
> > Hi Sujith,
> >
> > you can try to translate the initial configuration by, say, L/2 in all
> > directions using trjconv. If the bubble appears again at the edge, I
> > would suspect artifacts. If you are using Verlet cutoff scheme, you
> > can also try to change it to group - it helped in my simulation when a
> > droplet was pulled to the origin by a spurious force (
> >
> >
> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/6qnoy5o4/strange-behavior-of-water-droplet-on-a-solid-surface-with-verlet-cutoff-scheme-in-gmx-5-0-4
> > ).
> >
> > Regards,
> > Jan
> >
> > 2015-07-18 8:53 GMT+02:00 sujithkakkat . <sujithks58 at gmail.com>:
> > > Hello,
> > >
> > >  I am observing nucleation and growth of bubbles in a solution of
> methane
> > > in water with methane present at various levels of supersaturation.
> > >
> > > The system consists of a total 0f 2000 molecules in a cubic box with
> the
> > > number of CH4 varying from 80 to 200.  I am using a single point
> Lennard
> > > Jones potential for methane along with the TIP4P water model with short
> > > range interactions cutoff at 1.2nm.
> > >
> > >  Five different simulations were performed and in each case a methane
> > > bubble was formed . I find that in all cases the bubble is located near
> > the
> > > edge or a face of the box rather than being within the box. I wonder
> > > whether this is a coincidence or if it is an artefact. I am interested
> to
> > > know if someone had similar observations. Please comment.
> > >
> > > Regards,
> > > Sujith.
> > > --
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