[gmx-users] gromacs..

Henry Yang henryynag at yahoo.com
Wed Dec 9 15:28:17 CET 2009

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 

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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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