[gmx-users] Counting particles in a particular region

Steven Spronk spronk at its.caltech.edu
Thu Mar 25 22:18:01 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.

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!

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