[gmx-users] gromacs..

[XAvier Periole]

On Dec 9, 2009, at 3:41 PM, Justin A. Lemkul wrote:

>
>
> 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
You can obviously plot the box dimensions as function of time as  
suggested by Justin
and then multiply the X and Y component (if the membrane is in the xy  
plan) and divide
by the number of lipid per leaflet ...

>
> 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
>
> ========================================
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