[gmx-users] Area per lipid calculation

[Justin A. Lemkul]

NG HUI WEN wrote:
> Dear gromacs users,
> 
>  
> 
> I have a protein embedded in a lipid bilayer. After sufficient 
> equilibration of the system ( i.e. size of box X and Box Y became quite 
> constant), I would now like to assess the area per lipid of my system.
> 
>  
> 
> However, (I think) I could not simply do this  ( average size of box X * 
> average size of box Y/ number of lipids per monolayer) because there is 
> a protein in the middle of the bilayer. Ideally I would first like to 
> calculate the area occupied by the protein then take the difference 
> between the two as my answer. I notice this is how the inflategro script 
> calculates the estimated area per lipid during the shrinking process.  
> 
>  
> 
> I have had a search through the mailing list to look for an answer but 
> to no avail. It seems I might need a script to perform that?
> 

Shameless self-promotion:

http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

-Justin

>  
> 
> Thank you for your help.
> 
>  
> 
> HW
> 
> <<
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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

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