VMD-L Mailing List

From: Andrés Morales (h.andres.m1986_at_gmail.com)
Date: Thu Oct 20 2011 - 22:04:03 CDT

Dear VMD users:

 Is there anyone here to know how to calculate the area per lipid of a lipid
bilayer in a membrane system?
 Or, could anyone share the scripts to calculate them?

I was looking at VMD and NAMD mailing lists, and I found some suggestions to
calculate a crude approximation for area per lipid of a lipid bilayer .
According with those suggestions I wrote some simple scripts to calculate
them. But I have a problems. The calculated area per lipid for each frame
was around ~130 A^2 per lipid. It is a too large value since I am working
with a DPPC bilayer (~62 A^2 per lipid).

I calculated :
 Average area per lipid: "box size X * box size Y / no. of lipids" (lipids
are in the XY plane)

The scripts I use was (lipids 1 to 36 formed the monolayer above z=0 and
lipids 37 to 72 formed the monolayer beneath z=0 ):
**
*
set nf [molinfo top get numframes]
set sel [atomselect top "lipids"]
set sel1 [atomselect top all]
for {set i 0 } {$i < $nf } { incr i } {
    $sel frame $i

 $sel1 moveby [vecinvert [measure center $sel weight mass]]

 ## Area per lipid
 set min [lindex [measure minmax $sel] 0]
 set max [lindex [measure minmax $sel] 1]
 set minx "[lindex $min 0]"
 set miny "[lindex $min 1]"
 set maxx "[lindex $max 0]"
 set maxy "[lindex $max 1]"
 set lenght_x [expr $maxx - $minx]
 set lenght_y [expr $maxy - $miny]
 set area_por_lipido [expr ($lenght_x * $lenght_x) / 36]

*

Thanks for your suggestions

 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/