From: Adam Kells (adam.kells_at_ucdconnect.ie)
Date: Mon Jun 30 2014 - 06:49:07 CDT
Hi, I'm an undergraduate intern becoming acquainted with vmd and namd and I
am having trouble writing a code to find the centre of a ring of atoms in a
carbon nanotube. My code is:
proc radius molid {
set file [open "radius_[expr $molid].dat" w]
#Looping from 0 to 8 for the 9 rings that are in my nanotube.
for {set i 0} { $i <= 8} {incr i} {
#Initialise some variables
set sumr 0
set mass1 0
set com {0 0}
#There are 30 atoms per ring so i specify for this loop the ring of
interest.
set sel [atomselect $molid "index [expr $i*30] to [expr ($i*30)+29]"]
set sx [$sel get x]
set sy [$sel get y]
#Finding centre of mass.
foreach coord [$sel get {x y}] m [$sel get mass] {
set mass1 [expr ($mass1 + $m)]
set scaled [vecscale $m $coord]
set com [vecadd $com $scaled]
}
set centre [vecscale [expr 1. / $mass1] $com]
set cx [$centre get x]
set cy [$centre get y]
#Using coordinates of centre of mass to find the radius (distance of each
atom from the centre).
foreach x $sx y $sy {
set r [expr sqrt(($x - $cx)^2 + ($y - $cy)^2]
set sumr [expr $sumr + $r]
}
#Getting the average radius.
set rad [expr $sumr/19]
puts $file [list $rad]
}
close $file
}
The error I keep getting is "invalid command name "6.657242774963378e-5
0.0"".
Any help much appreciated.
Adam
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