[gmx-users] area per lipid

[Justin Lemkul]

On 11/8/12 4:39 AM, Shima Arasteh wrote:
> Hi,
>
> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the area  per lipid every 10 ns. The results of area per lipid in each step are as below:
>
> 1.
> Top leaflet: 60.44
>
> Bottom leaflet: 59.43
>
>
> 2.
> Top leaflet: 61.135
> Bottom leaflet: 60.11
>
> 3.
> Top leaflet: 61.40
>
> Bottom leaflet: 60.38
>
> 4.
> Top leaflet: 60.27
>
> Bottom leaflet: 59.27
>
> I expected it to approaches the expected amount steadily, but why did I get such a result? How can I get to the appropriate area  per lipid?
>
> Would you please give me suggestions? Any suggestions would be appreciated.
>

Without seeing a complete .mdp file, it's hard to say.  Why are you picking 
snapshots every 10 ns?  You can easily plot APL over time for the entire 
trajectory using the box vectors stored in the .edr file from (Box-X * 
Box-Y)/(number of lipids).  You would have to write your own script to do the 
calculation, but it's quite straightforward.

-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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