Selecting closest N water to ligand using trjorder

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GROMACS version: 2024.2-dev
GROMACS modification: No

Hi,
I’m trying to select closest N water molecules to ligand. I’m following this procedure:

  1. Produce ordered trajectory (ordered.trr) ordering on water group with trjorder.

  2. Extract first frame from ordered.trr (ordered.gro) and create index file (ordered.ndx); the I modify ordered.ndx creating new group (Water_Closest) using first 3N atoms of Water group.

  3. Create new index file (ordered_P-L-Closest-HOH.ndx) containing index for “protein | Ligand | Water_Closest”

  4. Extract, using trjconv, the atoms corresponding to group “protein | Ligand | Water_Closest” from ordered.trr

It’s seems that something went wrong, as visualizing trajectory, water molecules that, at beginning are around ligand, start wandering around.

Can I achieve desired result with this procedure?
Cloud be the problem the option “-s md.tpr” given to trjconv?

Any suggestion?

Best regards