Date: Tue Mar 27 2012 - 01:37:23 CDT


I want, for each molecule's center of mass, to extract its coordinates
into some file for every frame of simulation.
first,I load my_molecule_file.psf and my_molecule_file.dcd in VMD and then
I use my Tk console script:

set frm [molinfo top get numframes]
set atom [atomselect top "segid GLUB and resid 20"]
set fout [open Coords_CNTmas_GLUB_20.dat w]

for {set i 0} {$i<$frm} {incr i} {
$atom frame $i
set cntmas [measure center $atom weight mass]

puts $fout [format "%8.3f%8.3f%8.3f" [lindex $cntmas 0] [lindex $cntmas 1]
[lindex $cntmas 2]]
$atom delete
close $fout

I have got the results- the coordinates for each molecule but,I'm not sure
that everything is ok.
So, I will need a second hand opinion about my script, and is there
another way to get the coordinates of center of mass for each simulation's
frame for one or for whole group of molecules.