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

Alex Matyushov amatyush at asu.edu
Sat Aug 28 03:10:00 CEST 2010

Thanks. Do you mean the "-d" option? What exactly does it mean by "take the
normal on the membrane"? What membrane? What if I was simulating a system
that doesn't have any membranes?

Thank you,


On Fri, Aug 27, 2010 at 5:55 PM, Justin A. Lemkul <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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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