[gmx-users] cutting a cylinder from simulation box

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 28 00:55:19 CET 2012

On 28/02/2012 10:49 AM, Sanku M wrote:
> 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.

g_select can make such a selection from a trajectory frame and write it 
to an index file, but the diffusion of the water over time will be a 
problem for a static selection. The kind of dynamic selection you would 
want is not yet available. You could make do by scripting g_select and 
some subsequent analysis tool inside a shell loop.

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