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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Aug 28 04:30:31 CEST 2010

Dear Alex:

be careful with g_density! If you do not use the symmetrize -symm  
option, then the box height is going to be taken as a single frame. If  
you do NpT, then you will get an incorrect (or at least noisy) result.  
I forget if this will bite you if you do use the -symm option.

This is all to say that you should do some serious testing before you  
trust the plain output of this tool (or at least that was true in  

See, for example, the volume normalization, which is taken from a  
single frame in line 328,329 of src/tools/gmx_density.c, which are  
outside of the for loop over frames:

       (*slDensity)[n][i] = (*slDensity)[n][i] * (*nslices) /
         (nr_frames * box[axis][axis] * box[ax1][ax1] * box[ax2][ax2]);


-- original message --

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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