VMD-L Mailing List
From: Christopher Stiles (CS145331_at_albany.edu)
Date: Sun Mar 09 2008 - 14:55:51 CDT
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*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.
http://www.cs86.com/CNSE/SWNT/post_part7/SWNT_6_6_144_b4em.gro
http://www.cs86.com/CNSE/SWNT/post_part7/traj.trr
Thank you very much!
~Christopher Stiles
College of Nanoscale Science and Engineering (CNSE)
State University of New York, Albany, New York 12203, USA
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