VMD-L Mailing List

From: Stéphane Pezennec (stephane.pezennec_at_rennes.inra.fr)
Date: Wed Feb 23 2011 - 07:24:02 CST

Dear all,

It seems that the 'measure dipole' function (version 1.8.7) returns
erroneous results when:

- the net charge of the selection is not zero, and
- the center of mass of the selection is not at the origin, and
- the '-masscenter' flag is used.

As a side-effect, when the first two conditions are fulfilled, the
DipoleWatcher plugin displays incorrect dipoles.

It can be observed when the selection is moved (e.g., aligned on
something else, or simply translated using 'moveby'): the dipole, either
updated using the plugin or measured again using 'measure dipole
-masscenter', then changes in magnitude as well as orientation
relatively to the selection atoms. As far as I know, it should not.

I tried to look at the source (src/Measure.C, src/TclMeasure.C), but
could not see anything wrong.

I used a Q&D Tcl script to compute the dipole moment at the center of
mass:

  proc dpl {selection} {
          set cdm [measure center $selection weight mass]
          set p [veczero]
          set cht 0.0
          foreach pos [$selection get {x y z}] charge [$selection get charge] {
                  set p [vecadd $p [vecscale $charge $pos ]]
                  set cht [expr $cht + $charge]
          }
          puts $cht
          return [vecsub $p [vecscale $cht $cdm]]
  }

This script and 'measure dipole -masscenter' yield the same results only
when the center of mass of the selection is at the origin. On the few
proteins tested, the -masscenter dipole was very close to the
-origincenter one, whereas one could reasonably expect it to be close to
the -geocenter one.

As far as I can tell by using similar scripts, the use of the -geocenter
or -origincenter flags yields correct results, which points to the
computation of the center of mass.

I would be happy to help, by further testing or answering to more specific
questions.

Regards, 

-- 
Stéphane