[gmx-users] Counting particles in a particular region

David L. Bostick dbostick at physics.unc.edu
Thu Mar 25 23:26:01 CET 2004

Hi Steve

I wrote an analysis utility a while back and named it "g_occupancy." It's
description is as follows


g_occupancy can calculate the centers of mass of two groups of atoms
(groups 1
and 2) as a function of time.  It then counts the number of atoms in group
between these groups in the z direction.

Or when -radius is set, all the atoms in group 3 between groups groups 1
and 2
in z and within -radius (nm) in the xy plane of the vectorjoining groups 1

If you would like me to send it to you, let me know and I can do it outside
of the user list so as not to clutter it.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Thu, 25 Mar 2004, Steven Spronk wrote:

> Hi,
> 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.
> What I've found so far is that the program g_density comes the closest to
> what I want.  It can be used to calculate the number of particles in a
> slice through the whole simulation box, but I'm not sure you can specify
> restrictions in all three axes at once.  Also, g_density gives an average
> or a sum over a given duration; it doesn't give output as a function of
> time.  Are there options I can choose for g_density that will do what I
> want?  Or is there another program?
> Thanks a lot!
> Steve
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