[gmx-users] Time evolution of lipidbilayer

[Justin A. Lemkul]

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.

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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