AMBER Archive (2005)

Subject: AMBER: Meaning of induced dipole moments for atom pairs?

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed May 04 2005 - 15:52:06 CDT

Dear amber members,

I have done some dipole moment computations for a
covalently connected C-N atom
pair in a molecule.
I understand that the vectorial direction of
permanent
dipole moment for the atom pairs should be from N to C
(N ---> C) since N has more negative
partial charge than C. In that case, I guess N is the
center of mass for the atom pairs.

My question is about the induced dipole moment
computations for the atom pairs.
How would AMBER8 treat the atom pairs to compute an
induced dipole moment?
Is it something that AMBER8 computes induced dipole
moments for each atom separately
based on their polarizibility and the electric field
applied on each of the atoms, then the
induced dipole moments are summed up to yield a total
induced dipole moment for the atom pairs?

Or is it something that AMBER8 sees the atom pairs as
a whole ? Then what would be the polarizibility for
the whole system?

Another question, does AMBER8 needs to find a center
of mass to compute induced dipole moment
for a pair of atoms? (my answer would be "NO", but I
just want to make sure here)

Thanks,

jenk.

                
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