**From:** Andres Morales N (*andresmoralesn2_at_hotmail.com*)

**Date:** Mon Oct 17 2011 - 21:12:33 CDT

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Dear NAMD and VMD users:

Is there anyone here to know how to calculate the area per lipid and thickness for 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 aproximation for area per lipid and thickness of a lipid bilayer .

Acording with those suggestions I wrote some simple scripts to calculate them. But I have some problems.

First, the area per lipid calculated for each frame was around ~130 A^2 per lipid. It is a too large value since I am workin with a DPPC bilayer (~62 A^2 per lipid).

Second, the thickness calcualed was good for the 50 first frames, but for the other ones, it took too large values (~1000 A).

I calculated :

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

Thickness: I brought the membrane center of mass at origin (0,0,0), calculated average positive Z coordinates and average negative Z coordinates, substracted the negative from the positive

average.

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 ):

###################Protocol to calculate average Z coordinates ##########################

proc prom_z {sel} {

set sumz 0

foreach atom [$sel get index] {

set pos [lindex [[atomselect top "index $atom"] get {x y z}] 0]

set z1 [lindex $pos 2]

set sumz [expr abs($sumz )+ abs($z1)]

}

set promz [expr $sumz / 36]

return $promz

}

##############################################################################################

set mol [mol new dppc.psf type psf]

mol addfile dppc_eq.dcd type dcd waitfor all

set outfile [open Analysis_DPPC.txt w];

puts $outfile "Frame Area per lipid Thickness (N) Thickness (P)"

set nf [molinfo top get numframes]

set sel [atomselect top "lipids"]

set sel1 [atomselect top all]

set sel2 [atomselect top "lipids and resid 1 to 36 and element N"]

set sel3 [atomselect top "lipids and resid 37 to 72 and element N"]

set sel4 [atomselect top "lipids and resid 1 to 36 and element P"]

set sel5 [atomselect top "lipids and resid 37 to 72 and element P"]

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]

## Thicknes

set z1 [prom_z $sel2]

set z2 [prom_z $sel3]

set thinckness1 [expr abs($z1) + abs($z2)]

set z3 [prom_z $sel4]

set z4 [prom_z $sel5]

set thinckness2 [expr abs($z3) + abs($z4)]

puts $outfile "$i $area_por_lipido $thinckness1 $thinckness1"

}

close $outfile

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/

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