VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 17 2012 - 00:01:18 CDT

Hi,
  I assume that the error about the vectors having different sizes
is occuring for one of your vecsub calls. Have you checked to ensure
that you're not encountering some kind of error leading to one of the
selection queries trying to set an invalid frame or something similar?
I also noted that your script is starting at frame 500 rather than 0...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 16, 2012 at 11:16:31AM +0100, Ban Arn wrote:
> Dear VMD Users
>
> I'm using the following script to calculate lipid order parameter.
>
> mol new lipid_initial.pdb
> mol addfile lipid_traj.trr waitfor all
>
> proc orderparam-c3 { result { seltext all } } {
> upvar $result arr
> set n [molinfo top get numframes]
> for { set i 2 } { $i <= 20 } { incr i } {
> # puts $i
> set cp [atomselect top "($seltext) and lipid and name C3$i"]
> if { [$cp num] == 0 } {
> # puts "skipping $i"
> continue
> }
> set hx [atomselect top "($seltext) and lipid and name H${i}X"]
> set hy [atomselect top "($seltext) and lipid and name H${i}Y"]
> set hz [atomselect top "($seltext) and lipid and name H${i}Z"]
>
> set sum 0.0
> set nh 0
> set nres [$cp num]
> for { set frame 500 } { $frame < $n } { incr frame } {
> $cp frame $frame
> $hx frame $frame
> $hy frame $frame
> $hz frame $frame
> set cpx [$cp get x]
> set cpy [$cp get y]
> set cpz [$cp get z]
>
> set hxx [vecsub $cpx [$hx get x]]
> set hxy [vecsub $cpy [$hx get y]]
> set hxz [vecsub $cpz [$hx get z]]
> foreach dx $hxx dy $hxy dz $hxz {
> set norm2 [expr {$dx*$dx + $dy*$dy + $dz*$dz}]
> set sum [expr {$sum + $dz*$dz/$norm2}]
> }
> incr nh $nres
>
> if { [$hy num] != 0 } {
> set hyx [vecsub $cpx [$hy get x]]
> set hyy [vecsub $cpy [$hy get y]]
> set hyz [vecsub $cpz [$hy get z]]
> foreach dx $hyx dy $hyy dz $hyz {
> set norm2 [expr {$dx*$dx + $dy*$dy + $dz*$dz}]
> set sum [expr {$sum + $dz*$dz/$norm2}]
> }
> incr nh $nres
> }
>
> if { [$hz num] != 0 } {
> set hzx [vecsub $cpx [$hz get x]]
> set hzy [vecsub $cpy [$hz get y]]
> set hzz [vecsub $cpz [$hz get z]]
> foreach dx $hzx dy $hzy dz $hzz {
> set norm2 [expr {$dx*$dx + $dy*$dy + $dz*$dz}]
> set sum [expr {$sum + $dz*$dz/$norm2}]
> }
> incr nh $nres
> }
>
> }
> set arr($i) [expr {-1.5*$sum/$nh + 0.5}]
> puts [expr {-1.5*$sum/$nh + 0.5}]
> }
> }
>
> The script works fine for 30 frames and later shows error that the two
> vectors dont have the same size.
>
> I couldn't figure out. Kindly advice.
>
> Many Thanks
> Balaji 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078