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 <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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
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