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

[João Henriques]

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tool that does all of this in one step but I may be outdated regarding new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