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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