[gmx-users] Counting particles in a particular region
oliver at biop.ox.ac.uk
Fri Mar 26 12:00:01 CET 2004
> I am wondering if there's a function in Gromacs to count the number of
> particles in a particular region of my simulation box. In other words,
> I'd like to specify a particular range of all three coordinates, and for
> each timestep in my trajectory, count how many particles are in that
> smaller box. The ideal output would be the number of particles as a
> function of time. Specifically, I am running an MD simulation on an ion
> channel embedded in a lipid bilayer, and I'd like to determine the water
> occupancy of the pore region, and how it changes through the trajectory.
I had exactly the same problem and wrote `g_count' for that purpose. It is
fairly horrible code (my first gromacs program and the second in C... go
figure) but it has been producing results over the last 2 years.
You specify a cylindrical region and an index group and you get the
occupancy of this region over time.
I can send you a tar ball with the code, just email me. It will also
include g_flux which counts full transitions of the pore, useful when you
want to calculate equilibrium fluxes. (You might also find `gridcount'
useful, see the gromacs contributions page).
Oliver Beckstein * oliver at biop.ox.ac.uk
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