VMD-L Mailing List

From: Christopher Stiles (CS145331_at_albany.edu)
Date: Thu Aug 09 2007 - 09:11:55 CDT

I have been trying to come up with a script for radial density over the
whole run but it have been just giving me zeroes, if some one could take a
quick look at let me know if any errors catch there eye right away that
would be great.

 

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

set nt [atomselect top "resid 1"]

set NT_min [lindex [lindex [measure minmax $nt] 0] 2]

set NT_max [lindex [lindex [measure minmax $nt] 1] 2]

set NT_radius 0

set NT_radius_old 0

set num_frames [molinfo top get numframes]

set x_list {}

set y_list {}

set step_size 7.5

set NT_radius_max 15

 

 

set wat_sel [atomselect top "water and (z > $NT_min and z < $NT_max and
sqrt((x*x) + (y*y)) < $NT_radius and sqrt((x*x) + (y*y)) > $NT_radius_old)"]

 

while { $NT_radius <= $NT_radius_max } {

set NT_radius_old $NT_radius

set NT_radius [ expr { $NT_radius + $step_size } ]

set holder 0

 

for {set i 0} {$i < $num_frames} {incr i} {

$wat_sel frame $i

$wat_sel num

$wat_sel update

set holder [ expr { $holder + [ $wat_sel num ] } ]

}

 

lappend x_list $NT_radius

lappend y_list $holder

}

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

 

Thank you,

~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New York 12203, USA