[gmx-users] Location of Bubbles.

Jan Jirsák janjirsak at gmail.com
Sat Jul 18 09:49:17 CEST 2015

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 (


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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