[gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin ! That is APL. How about bilayer thickness ? I made
density.xvg file of headgroup from using g_density.


On Mon, Jan 21, 2013 at 7:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/13 5:12 AM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> I want to know that my lipid bilayer is equilibrated or not yet. So i want
>> to calculate the change of area per lipid and the bilayer thickness versus
>> time.
>>
>> Which tool or method should i use ?
>>
>>
> Extract box vectors over time from the .edr file, then use a script of
> your own creation to multiply them and divide by the number of lipids per
> leaflet.  Of course, that goes out the window if there is a protein present.
>
> -Justin
>
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> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
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