O
UT

OF

PLANE
B
ENDING
I
NTERACTIONS
I
Outofplane interactions are closely related to the torsional
terms
I
For four atoms (A,B,C,D) which for three angles (ABC, ABD,
CBD), there can be an energy cost for moving one of the atoms
out of the plane spanned by the three other atoms
I
This can be accounted for in one of two main ways:
I
Harmonic potential
I
Improper torsion term
N
ON
B
ONDING
I
NTERACTION
I
Nonbonded interactions act both between atoms in the same
molecule and those in other molecules
I
These are often divided to
I
Electrostatic interactions
I
Van der Waals interactions
I
The electrostatic part arises from charge differences within a
molecule
I
This can be modeled by distributing point charges in the
molecule
I
Of course, the simple approach is to implement an interaction of
the form (CHARMm & AMBER)
U
elect
=
1
4
πε
0
q
1
q
2
r
ij
(6)
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I
Also a dipoledipole interaction can be implemented to act
between polar groups
I
A functional form is (MM2):
U
e
=
μ
i
μ
j
ε
0
r
3
ij
{
cos
χ

3 cos
α
i
cos
α
j
}
(7)
The
μ
i
,
j
are dipole moments,
χ
is the angle between them. The
α
i
,
j
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 Winter '12
 Kotakoski
 Atom, Molecule, Van der Waals, Buckingham

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