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6. The modified values of K sres and BL res are
used in the molecular mechanics portion of the
MM2 computation to further refine the
molecule.
Stretch-Bend Cross Terms
Stretch-bend cross terms are used when a coupling
occurs between bond stretching and angle bending.
For example, when an angle is compressed, the
MM2 force field uses the stretch-bend force
constants to lengthen the bonds from the central
atom in the angle to the other two atoms in the
angle.
1
Ε= ∑
2 K sb( r − r o
)θ − θ o
Stretch / Bend
( )
The force constant (K sb ) differs for different atom
combinations.
The seven different atom combinations where
force constants are available for describing the
situation follow:
• X-B, C, N, O-Y
• B-B, C, N, O-H
• X-Al, S-Y
• X-Al, S-H
• X-Si, P-Y
• X-Si, P-H
• X-Ga, Ge, As, Se-Y, P-Y
where X and Y are any non-hydrogen atom.
User-Imposed Constraints
Additional terms are included in the force field
when constraints are applied to torsional angles and
non-bonded distances by the Optimal field in the
Measurements table. These terms use a harmonic
potential function, where the force constant has
been set to a large value (4 for torsional constraints
and 10 6 for non-bonded distances) in order to
enforce the constraint.
For torsional constraints the additional term and
force constant is described by:
Ε= ∑ 4(θ − θ o
) 2
Torsions
For non-bonded distance constraints the additional
term and force constant is:
Ε= ∑ 10 6
(r − r o
) 2
Distance
Molecular Dynamics
Simulation
In its broadest sense, molecular dynamics is
concerned with simulating molecular motion.
Motion is inherent to all chemical processes. Simple
vibrations, like bond stretching and angle bending,
give rise to IR spectra. Chemical reactions,
hormone-receptor binding, and other complex
processes are associated with many kinds of
intramolecular and intermolecular motions. The
MM2 method of molecular dynamics simulation
uses Newton’s equations of motion to simulate the
movement of atoms.
Conformational transitions and local vibrations are
the usual subjects of molecular dynamics studies.
Molecular dynamics alters the values of the
intramolecular degrees of freedom in a stepwise
fashion. The steps in a molecular dynamics
simulation represent the changes in atom position
over time, for a given amount of kinetic energy.
The driving force for chemical processes is
described by thermodynamics. The mechanism by
which chemical processes occur is described by
kinetics. Thermodynamics describes the energetic
relationships between different chemical states,
whereas the sequence or rate of events that occur as
molecules transform between their various possible
states is described by kinetics.
138•Computation Concepts
CambridgeSoft
Molecular Mechanics Theory in Brief