[gmx-users] cutting a cylinder from simulation box

[Jianguo Li]

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 <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
 

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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