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

[Justin Lemkul]

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

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