Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 9 15:41:12 CET 2009
Henry Yang wrote:
> Hi there,
> Thanks for telling how to calculate the area per lipid. But at the same
> time if I want to draw a plot of area per lipid vs time then how can I
> proceed? Any gromacs tool comes out which I can use? thanks
No. As I said in my previous message, you will have to come up with some script
(or use some other software) to multiply those box vectors and divide by the #
of lipids per leaflet. You can then plot those derived data.
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tue, December 8, 2009 12:49:18 PM
> *Subject:* Re: [gmx-users] gromacs..
> Henry Ynag wrote:
> > Hello everyone,
> > I am quite new to gromacs. I would like to know how can I calculate
> the area per lipid for my simulations. I am running simulations with 128
> DMPC lipid bilayer. I have the output of 30 ns simulations. Also how
> can i make a graph with this output.
> Plot the relevant box vectors from the .edr file (g_energy). You then
> have to come up with your own way to multiply these values (to get the
> total lateral area) and divide by the # of lipids per leaflet. A simple
> Perl script should do the trick.
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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