[gmx-users] Location of Bubbles.

[Jan Jirsák]

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.
> --
> 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.