[gmx-users] Different values of area per lipid with/without protein

[Justin Lemkul]

On 8/23/12 1:39 PM, Kulleperuma Kulleperuma wrote:
>
>
> Hi all
>
> I embedded the protein in POPC using inflategro. After the desired area per lipid (APL-0.64 A2) is reached I recalculated the APL with and without the protein.
> I get two different values; with the protein - 0.64 and without the protein - 0.82.
> I ran perl inflategro input.gro 1 POPC 0 output.gro 5 area.dat to get the above values.
>
> I was expecting to get the same values for the two cases. Can someone explain the reason for this difference, since inflategro subtract the area of the protein in any case.

If there is a protein present and lipids have been removed, some portion of the 
membrane plane is no longer occupied by lipids.  You're dividing the total area 
by fewer lipids, so the area goes up.

-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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