VMD-L Mailing List

From: Stéphane Pezennec (stephane.pezennec_at_rennes.inra.fr)
Date: Thu Feb 24 2011 - 03:05:22 CST

Le mercredi 23 février à 13h55 (-0600), John Stone a écrit :

> I took a close look at this, and I think I've found what's going
> wrong with the -masscenter case:
> double mscale = totalq / (totalm * sel->selected);
>
> This is dividing by both total mass and by the number of selected
> atoms, I believe it should only be dividing by total mass:
> double mscale = totalq / totalm;
>
> This should account for the difference between the Tcl proc Stephane
> wrote vs. the output from "measure dipole" with -masscenter.
> I will double check this and commit the fix if I didn't miss something
> here.

Dear all,

I was not sure about the meaning of 'sel->selected' when I looked at
Measure.C, but I think that John is right: the division by the number of
atoms is justified in the 'geometrical center' case (which works
correctly), but not in the 'center of mass' case.

In a quick test, a modified script (see below) with the extra division
by the number of atoms gives the same (incorrect) result as the old
'measure dipole -masscenter'.

Thanks and congratulations for your reactivity!

Regards,

Stéphane

[Tcl]
  proc dipoleX {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 [expr $cht / [$selection num]] $cdm]]
  }
[/Tcl] 

-- 
Stéphane Pezennec