[gmx-users] Self-interaction across periodic boundaries

[Mark Abraham]

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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