AMBER Archive (2005)Subject: AMBER: Induced dipole in AMBER8
From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Apr 22 2005  11:57:56 CDT
Dear Amber community,
I have a question about the way that induced dipole is
implemented in the sander module of AMBER8.
When I looked in
$AMBERHOME/src/sander/prn_dipoles.f
I saw that
Indiptotal = sqrt((inddipx^2)+(inddipy^2)+(inddipz^2))
However, I have not seen any definition for
inddip(x,y,z) array in prn_dipoles.f .
Could someone please formulate inddip used in sander?
Isn't it proportional to field strength
(E*=E.COS(teta) where E is an electric field)and
polarizibility (alpha) [inddip = alpha.E*]?
If this is correct then what would be the value of E
for an atom group of a molecule immersed in POL3BOX.
One could also apply Debye's formula for a dilute
solution in a nonpolar solvent to determine induced
dipole and polarizibility as a function of temperature
and other variables such as dielectric constant,
viscosity, molecular weight, etc., but I am
not exactly sure if inddip in sander works like that.
best regards,
Jenk.
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