[gmx-users] Plotting area per lipid along time

[Justin Lemkul]

On 10/21/12 8:47 AM, Shima Arasteh wrote:
> Hi,
>
> Would you please give me an advice to get area per lipid plot as a function of time?
>
> I'm only able to get area per lipid from the .gro file of mdrun, but I don't know if it is possible to see the all area per lipids along the time?
>

If you have a pure lipid system, then APL is calculated as the product of the 
x-y box vectors (assuming that the membrane is in the x-y plane) divided by the 
number of lipids per leaflet.  This method does not allow you to obtain the 
areas contributed by each individual lipid.  If you have a protein present, 
there is no Gromacs tool that will allow you to do this calculation at all 
because you need the area of the protein.

If you are using our GridMAT-MD program, you can loop the script over individual 
snapshots using simple shell scripting.  We intend to include trajectory support 
at some point in the future, but none of the current developers have much time 
to work with it right now.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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