[gmx-users] gromacs..

[Justin A. Lemkul]

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.

-Justin

> Henry
> 
> ------------------------------------------------------------------------
> *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
> 
> -- ========================================
> 
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

========================================