[gmx-users] insert-molecules results in molecules sticking out of box, could "solvate" face an issue?

Mark Abraham mark.j.abraham at gmail.com
Mon May 14 04:23:38 CEST 2018


The more molecules there are in a periodic box, the more likely it is that
all of the equivalent representations of it with whole molecules have at
least one molecule crossing such a boundary. That is, the tool is built for
that normal case of whole molecules not all of which are contained within
the current boundaries. Of course, there will need to be a matching gap on
the far side of the box, which the tool understands.


On Mon, May 14, 2018, 00:22 Anuradha Bhat <anur.bhat at gmail.com> wrote:

> Hi
> I inserted 20 copies of a solute molecule into a box. Some of the molecules
> are partly sticking out of the box. I would like to solvate this box.
> However, I read that one of the known issues with gmx solvate is that
> "molecules
> must be whole in the initial configurations." So, is it okay if the solute
> molecules are sticking out of the box when using gmx solvate?
> Thanks in advance,
> Annu.
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