[gmx-users] Self-interaction across periodic boundaries

[Salman Zarrini]

Thanks Mark.
The problem is that I would like to keep the overall concentration
constant, so, using a larger box e.g. with 2 times larger lateral box
dimensions,
needs me to increase the number of molecules 8 times, so even more likely
to lead to percolating structures in a larger simulation box.

Best regards,
Salman Zarrini

On Mon, Jul 8, 2019 at 6:24 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you're trying to model something like it was at infinite dilution using
> a periodic box, then the size of the box needs to be at least as large as
> the size of the structure and its effective interaction radius. It seems
> like your simulation is suggesting at least one of those is larger than you
> first thought it was :-)
>
> Mark
>
> On Mon, 8 Jul 2019 at 11:58, Salman Zarrini <salman.zarrini at gmail.com>
> wrote:
>
> > Dear all,
> > Using MD simulations I expect to observe aggregation among some molecules
> > solvated in water to have ultimately a droplet out of the molecules. The
> > aggregates form to some extent in the course of simulation time, however,
> > after a while the system become kinetically trapped in artificial
> > percolating aggregates in which the molecules are self-interacting across
> > the periodic boundaries.
> > I wonder if there is any possibility to prevent aggregates
> self-interaction
> > across periodic boundaries?
> >
> > Thank you,
> > Salman
> > --
> > Best regards,
> >
> > Salman Zarrini
> > --
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