[gmx-users] g_density?

[Justin A. Lemkul]

minnale wrote:
>  
> Hi all,
>     I have small doubt on g_density, The bilayer thickness can be 
> estimated by calculating density profile here I have calculated density 
> for different groups in lipid system by g_density command.
> 
>   The POPC density profile x-axis(z-nm) vs y-axis(density), it looks "M" 
> shape what is it mean first high and second high peak exactly?   
> 

Which axis are you analyzing?  "x-axis(z-nm)" makes no sense to me.  Is your 
bilayer in the x-y plane (the canonical view), or does it have some other 
orientation?

Your output also depends on what you've analyzed.  Was it the bilayer as a 
whole?  Just acyl chains?  Headgroups?

Whatever it is that you've analyzed, the output corresponds to the density 
(kg/m^3) of that species at that point along the box dimension.

> My idea is based on literature survey first peak tells one half of the 
> bilayer density and other peaks tells remain half of the bilayer 
> density.am I right?
> 

So you're saying that the overall bilayer density should be the sum of the two 
peaks you're seeing?  I guess the proper interpretation will depend on the 
answers to the questions I've posed above.

-Justin

> Any suggestions would be appreciated.
> 
> Thanks in adavance
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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