[gmx-users] Solvating only part of a box

[Mark Abraham]

Hi,

The default behaviour is to consider atom positions, but you want to
include atoms based on e.g. molecule position. IIRC use -selrpos mol_cog
for that (or similar changes within the selection). See the final examples
at
http://manual.gromacs.org/documentation/2018/onlinehelp/selections.html#selection-examples

Mark

On Thu, Sep 27, 2018 at 8:28 PM Alex <alexanderwien2k at gmail.com> wrote:

> 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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