• ## Outreach

From: Christopher Stiles (CS145331_at_albany.edu)
Date: Sun Mar 09 2008 - 14:55:51 CDT

*Sorry if this has posted twice I looked though the list and it did not seem
to have gone through,*

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.

Please note that as of now I am just trying to get it to run over one frame,
looping is not a problem.

#*****************************************************************

#*****************************************************************

#*****************************************************************

#Put following code into the Tk console

#*****************************************************************

#*****************************************************************

#*****************************************************************

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 x_0 [lindex [measure center \$nt] 0]

set y_0 [lindex [measure center \$nt] 1]

set step 0.25

set num_frames [molinfo top get numframes]

set Inner_limmit 0

set Outer_limmit 0

set numb {0}

set x 1

set y 0

for {set i 1} {\$i < 1000} {incr i} {

set y "[expr \$i + \$x]"

set numb [linsert \$numb \$y 0]

}

llength \$numb

#*****************************************************************

#*****************************************************************

#*****************************************************************

#Put following code into the black VMD command window

#*****************************************************************

#*****************************************************************

#*****************************************************************

set wat_sel [atomselect top "water and (z > \$NT_min and z < \$NT_max and
sqrt((x-\$x_0)*(x-\$x_0) + (y-\$y_0)*(y-\$y_0)) <= \$Outer_limmit and
sqrt((x-\$x_0)*(x-\$x_0) + (y-\$y_0)*(y-\$y_0)) > \$Inner_limmit)"]

#*****************************************************************

#*****************************************************************

#*****************************************************************

#Put following code into the Tk console

#*****************************************************************

#*****************************************************************

#*****************************************************************

for {set j 0} {\$j < 1000} {incr j} {

set Inner_limmit "[expr \$j*\$step]"

set Outer_limmit "[expr \$j*\$step + 1*\$step]"

lreplace \$numb \$j \$j "[expr [lindex \$numb \$j] + [\$wat_sel num]]"

}

#*****************************************************************

#*****************************************************************

#*****************************************************************

#this last bit of code should of stored density of water of the box in
relation to the center of the box in the "numb" list.

#*****************************************************************

#*****************************************************************

#*****************************************************************

The following are links to the files I use.

Thank you very much!

~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

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