[gmx-users] Counting particles in a particular region

David spoel at xray.bmc.uu.se
Thu Mar 25 22:39:01 CET 2004

On Thu, 2004-03-25 at 22:17, 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?
Don't think so. Your best bet is to modify g_density for your needs.
(File gmx_density.c)

> Thanks a lot!
> Steve
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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