[gmx-users] How to control and interpret g_density analysis more precisely?
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 28 03:15:32 CEST 2010
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.
> Thank you,
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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