[gmx-users] rmax and amax options of g_densmap

Rebeca García Fandiño regafan at hotmail.com
Wed Feb 17 20:15:32 CET 2010

I would like to calculate the density maps for the water inside a pore that has a cilindrical shape, but not the water outside it, that is also present in the box.
I don´t understand vey well the options of g_densmap "-amax" and "-rmax". With -amax I define the maximun axial distance from the center, let´s say the principal axis of my pore. With -rmax, I define the maximun radial distance, but is this in a perpendicular direction to the axis? or also in 3 directions? Because, if it is in 3 directions, and my pore is cilindrical (not spherical), so rmax >> amax, there will be a region that is not going to be taking into account for the density calculation...
Could anybody explain a little more about rmax and amax options of g_densmap, please?
Thank you very much in advance.
Best wishes,

Rebeca Garcia.
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