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 . <sujithk...@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-requ...@gromacs.org. -- 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-requ...@gromacs.org.