VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Mar 02 2007 - 07:41:25 CST

On Fri, 2 Mar 2007, Per Jr. Greisen wrote:

PG> Hi,
PG>
PG> I am trying to calculate the dipole moment and the dipole vector for a
PG> protein in VMD. So I have made a script getting the charge from PSF and

how about using the 'measure dipole'?

PG> using the formula
PG>
PG> \mu = \sum 4.8*Q_a * R_ab
PG>
PG> to compute the size of dipole-moment where the summation is over all the
PG> atoms including hydrogen. My problem is that I get a huge number out in
PG> Debye and I do not have big confidence in the number - is the formula
PG> correct?

basically yes. you only have to decide what to do, if the molecule is
charged. the usual convention is to subtract the position vector
of the gemetrical center of the molecule times the total charge
from the dipole vector and then take the absolute to compute the
total dipole.

PG> Assuming dipole moment is correct - one can relate the size of the dipole
PG> moment with the size of ones unit cell and the size of periodic boundary
PG> conditions?

the dipole moment of a molecule should not depend on its position
and/or the size of the simulation box. before computing the dipole
moment from a PBC calculation, you thus have to make sure that all
atoms of the molecule are selected that you use the closest image to
the center of the molecule.

generally, you should see the dipole as part of a multipole expansion
describing the charge distribution starting with the net charge
as the zeroeth moment...

cheers,
   axel.

PG>
PG> Any suggestions appreciate. Thanks in advance
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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If you make something idiot-proof, the universe creates a better idiot.