[gmx-users] cutting a cylinder from simulation box
Mark.Abraham at anu.edu.au
Tue Feb 28 00:55:19 CET 2012
On 28/02/2012 10:49 AM, Sanku M wrote:
> 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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