henryynag at yahoo.com
Wed Dec 9 15:28:17 CET 2009
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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