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

[Mark Abraham]

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 tool that does all of this in one step but I may be outdated regarding new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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