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