[gmx-users] picking out resident water molecule?

Yun Shi yunshi09 at gmail.com
Sat Nov 12 07:56:12 CET 2011

Hi everyone,

I am doing MD simulation with a protein-ligand system, and I want to pick
out the water molecules (their residue numbers or coordinates in any frame)
that simultaneously contact (within 0.4 nm range for heavy atoms) the
ligand and the protein, so that I could plot the lifetime of these resident
water molecules within a trajectory.

Does anyone know how to achieve this within GROMACS?

Thanks for any advice.
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