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

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 28 02:55:45 CEST 2010

Alex Matyushov wrote:
> 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.

I would suggest that you start by reading the contents of g_density -h.  There 
you will see the default options (one of which happens to be the box dimension 
along which the density is calculated).  You should never run a command blindly, 
hoping to get an answer.  The manual has implementation details for many of the 
algorithms that the tools utilize, information that will help you make wise choices.


> Thanks!
> Alex


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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