[gmx-users] All water molecules inside protein

Dawid das addiw7 at googlemail.com
Sun Feb 3 11:09:43 CET 2019

Dear Gromacs Users,

I need to extract gro or pdb file with single snapshot from a trajectory
for a protein inside solvation box. In the output, I need whole protein
structure + all water molecules "inside" the protein. That could also mean
all water molecules within let's say 0.3 nm distance from any atom
belonging the protein. What is a simple and effective way to find only
those water molecules which are within 0.3 nm distance from protein, please?

Best wishes,
Dawid Grabarek

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