[gmx-users] Time evolution of lipidbilayer

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 9 13:58:17 CEST 2008

minnale wrote:
> Hi all,
>   This may be a trivial question
>     I want to calculate "time evolution of area per lipid"
> The steps I have done are
> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy 
> command.
> 2. I have written code for calculating area per lipid in way that boxX 
> multiply with boxY divided by 64
> 3. I have got the plot in this way
>     **0 to 1000ps ---- started the value 0.609678 nm^2/N ended with 
> 0.642679(shows high peak)
>     **then 1000 to 4000ps  shows silght variation with 0.64 value( 
> nearly straight line)
>     **at 4000ps the value increased to 0.653465 ( high peak) from 
> there it reduced again to 0.647856 
> I want to ask you that the way values are got correct? and suggest me 
> some articles regarding area per lipid

Your calculations seem reasonable, and you could also concatenate your 
trajectories to get one continuous plot to make things simpler.  The 
value seems about right for POPC, but it's been a while since I checked 
the exact number.

As far as literature goes, a simple Google search will turn up lots of 
useful results.  And if you're using the lipid parameters from 
Tieleman's site, his publication list is a good place to start.


> Thanks for your aprreciation.
> Amity
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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