[gmx-users] Location of Bubbles.

[Mark Abraham]

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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