[gmx-users] How to control and interpret g_density analysis more precisely?

Alex Matyushov amatyush at asu.edu
Sat Aug 28 02:45:57 CEST 2010

Dear Gromacs community,

I've been using g_density to analyze distribution of atoms in an elongated
box with a lipid bilayer and lipid monolayers at each end of the box. My
results suggest that it found the density along the z-coordinate, which is
the longest dimension in the box. That is indeed what I wanted but how would
I check for sure what exactly it did? Or what if I wanted to find the
density distribution in a different direction in the box? Say I wanted it as
a function of coordinates in the x-direction. How would I specify it?

Overall I'd just like to have a better understanding and control over what
exactly g_density is doing because right now I feel that I'm just getting
some numbers out but who knows how.


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