From: Axel Kohlmeyer (
Date: Wed Mar 19 2008 - 07:32:17 CDT

On Wed, 19 Mar 2008, Alessio Alexiadis wrote:

AA> Hi everybody,

hi alessio,

AA> Do you know how to calculate with VMD the dipole moment of a
AA> molecule from a .cube file? I have a certain number of water

there is not (simple) way to do this from VMD. you need
a way to partition the electronic densities. it is usually
much easier to do this from the code that produces the
cube file (which code?).

AA> molecule and relative electronic densities and I want to calcolate
AA> the electric dipole of every molecule.

hmmm... what are relative electronic densities?

there is a number of way to compute the dipole moment.
- based on partical charges as a result of a population analysis
- based on maximally localized wannier function centers (plus
  atom core charges and positions).
- based on charge derived from an independent method.

if you have no more access to the original calculation,
your options are severly limited. what might work is to
use the bader analysis code from the henkelman group:, but that requires
the full all-electron density to work correctly.


AA> Thanks in advance
AA> Alessio
AA> ---------------------------------
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.