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
--
========================================
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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