[gmx-users] Solvating only part of a box

[Alex]

Thanks Mark.
The gmx select and then gmx trjconv work fine and I have a box with a more
or less desirable region being solvated by water.
However there is only one problem and that is the SOL's molecules in the
border of the region ( resname SOL and z>= 2 ). By that the Water molecules
in the border are split;  for instance a OW and one HW1 are in one side of
the border (to be considered in the gmx select) and the HW2 is in another
side of the border (to not be considered in the gmx select). Do you know
how I can either consider or discard those whole SOL's OW,HW1 and HW2 all
together?

Thanks.
Alex


On Thu, Sep 27, 2018 at 12:20 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> No, but you can use gmx select to make such a selection from the
> fully-solvated box, and gmx editconf (maybe) or gmx trjconv (definitely) to
> end up with the content you want. (We'd like to make this functionality
> more generally available, but it's not ready yet...)
>
> Mark
>
> On Thu, Sep 27, 2018 at 6:10 PM Alex <alexanderwien2k at gmail.com> wrote:
>
> > Dear all,
> > I wonder if it is possible to solvate just a part of a box using gmx
> > solvate. For example suppose you have a box with the lengths of x, y, z,
> > then, how I can solvate only a part of it like (x, y, z with z> 2)?
> >
> > Thanks
> > Alex
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