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

[Justin Lemkul]

On 1/21/13 10:17 AM, Kieu Thu Nguyen wrote:
> Thank Justin ! That is APL. How about bilayer thickness ? I made
> density.xvg file of headgroup from using g_density.
>

g_dist with index groups specifying however you want to define the boundaries 
for the membrane, or (shameless plug) a lateral projection of thickness (from 
which an average can easily be derived: http://bevanlab.biochem.vt.edu/GridMAT-MD/.

-Justin

>
> 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
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================