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

[Justin A. Lemkul]

Alex Matyushov wrote:
> Thanks. Do you mean the "-d" option? What exactly does it mean by "take 

Yep, that's the one.

> the normal on the membrane"? What membrane? What if I was simulating a 
> system that doesn't have any membranes?
> 

The g_density tool only really makes sense for interfacial-type systems like 
membranes.  For a simple protein-in-water system, the value of the density will 
be basically flat, and equal to the density of the solvent.  You can extract the 
same information in a more meaningful way from the .edr file.

Based on your description (a monolayer at the two ends of the box, presumably 
then interacting via PBC), I'd say you've got a membrane, more or less, but in 
any case, the interpretation of the results is the same.

-Justin

> Thank you,
> 
> Alex
> 
> 
> On Fri, Aug 27, 2010 at 5:55 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
>     -Justin
> 
>         Thanks!
> 
>         Alex
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================