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.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
