From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Feb 05 2007 - 14:26:10 CST
Himanshu,
Have a look at this previous message by JC:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7014.html
I would add that starting structures shipping with the plugin are already
interdigitated, which requires additional caution. You may want to search the
web for other, nicer starting points for your bilayers (e.g., the websites of
Scott Feller and Mikko Karttunen).
Jerome
On Monday 05 February 2007 12:50, Himanshu Khandelia wrote:
> If one generates a POPE membrane using the vmd plugin, the resulting area
> per lipid is about 71 A^2 per lipid [example, a 100 x 100 patch has 140
> lipids in each leaflet]. This area per lipid is about 17% higher than the
> experimentally measured values at 30-40 degree C. However, the average
> bilayer thickness (phosphate-to-phosphate) is about 38 A, which is more or
> less as expected in experiments.
>
> It this initial membrane setup not too far from equilibrium ? Of course,
> one could equilibrate to the correct area per lipid, but that would
> require holding the headgroups constrained along the bilayer normal, so
> that the bilayer thickness does not increase while the area gets reduced.
>
> However, I have not really come across this method/discusssion/problem in
> any articles where VMD's plugins have been used. What am I missing ?
>
> -Himanshu
>
> P.S: I think this post is relevant to both vmd and namd forums, and have
> copied it to both.
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