From: Jelle van Sijl (j.vansijl_at_gmail.com)
Date: Wed Feb 03 2010 - 11:21:33 CST

Dear All,
I would like to compute the molecular dipole moment for a given
selection of atoms. The IONS+CENTERS.xyz file contains 4 Wannier centers
per H2O molecule identified by atom name "X".

I've searched the vmd list archive and so far came up with creating a
user field selection of WFC values:

package require pbctools
  set mol [mol new {GEOM.xyz} waitfor all]
  mol addfile {IONS+CENTERS.xyz} waitfor all
  set mol [molinfo top]
  pbc set {12.50 12.50 12.50} -all

  set xsel [atomselect $mol "name X"]
  set nf [expr [molinfo $mol get numframes] - 1 ]
  set nx [$xsel num]
  set fp [open "WANNIER_CENTER" "r"]
  
  for {set f 0} {$f < $nf} {incr f} {
    set ul {}
    for {set i 0} {$i < $nx} {incr i} {
      gets $fp line
      lappend ul [lindex $line 1 2 3 4]
      }
    $xsel frame $f
    $xsel set user $ul
  }
  close $fp

which gives the following error message:
atomsel: set: bad data in 0th element

How can I select the right WFC's given a selection of atoms?
Once I have the WFC's in a selection, how can I use vmd to combine these
with the ion positions such that I get the average dipole moment per
H2O?

Thanks in advance & kind regards,
Jelle van Sijl

-- 
Jelle van Sijl, MSc.
PhD student, Department of Petrology
Faculty of Earth and Life Sciences (FALW)
VU University Amsterdam, De Boelelaan 1085
1081 HV Amsterdam, The Netherlands
Phone +31 (0)20 5983725
http://www.falw.vu.nl/petrology