[gmx-users] Remove all but N closest water molecules from protein

[Jose Borreguero]

Hi Mark,

The following lines select solvent molecules within some cutoff distance of
the protein:

close_solvent_atoms = group "SOL" and within 0.5 of group "Protein";
close_solvent_molecules = same resindex as close_solvent_atoms;
"strippedSystem" group "Protein" or close_solvent_molecules;

It's not exactly what I wanted, butI can select N closest water molecules
by tuning the cutoff distance.

.Jose

On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Or gmx select to make an index group for the nearest waters, and gmx
> trjconv to make the subset with the index group.
>
> Mark
>
> On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> joao.m.a.henriques at gmail.com>
> wrote:
>
> > Hi,
> >
> > trjorder can reorder the water molecules in each frame according to their
> > distance to the protein. Then you either manually prune the gro file(s)
> or
> > use an index file to get rid of the extra stuff. I don't know of any
> native
> > tool that does all of this in one step but I may be outdated regarding
> new
> > stuff on gmx 2016.
> >
> > Cheers,
> > João
> >
> > On Jun 8, 2017 2:49 AM, "Jose Borreguero" <borreguero at gmail.com> wrote:
> >
> > Dear Gromacs users,
> >
> > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
> > me to create a new *.gro file containing the protein and the N closest
> > water molecules to the protein
> > ​, starting from a system of a solvated protein​
> > ?
> >
> > Best,
> > Jose Borreguero
> > --
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