[gmx-users] cutting a cylinder from simulation box

Jianguo Li ljggmx at yahoo.com.sg
Tue Feb 28 02:29:58 CET 2012

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

 From: Sanku M <msanku65 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, 28 February 2012, 7:49
Subject: [gmx-users] cutting a cylinder from simulation box

  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.
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