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

Justin Lemkul jalemkul at vt.edu
Mon Jan 21 13:31:44 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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