Maybe you can try "trjorder" to order the water molecules around your protein
and make a group of those nearest water molecules and output them using trjconv
Jianguo
________________________________
From: Sanku M <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Tuesday, 28 February 2012, 7:49
Subject: [gmx-users] cutting a cylinder from simulation box
Hi,
I have run a simulation of a fixed object in water using gromacs. Now, I want
to analyze only water molecules which are present within a cylinder of certain
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the
particles within a cylindrical volume of a simulation box.
Thanks
Sanku
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