[gmx-users] calculate area per lipid and bilayer thickness versus time
jalemkul at vt.edu
Mon Jan 21 17:03:07 CET 2013
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/.
> 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
>>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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