A D V A N C E D E N G I N E E R I N G T H E R M O D Y N A M I CS

Molecular Dynamics
1) What is the classical molecular mechanics? Which are the fundamental equations underlying this
modeling approach?

Classical Molecular Mechanics (MM) is the application of Classical Mechanics to model

molecular systems, systems described in the scale of nm and ns. In this modeling approach each
atom is simulated as a single particle at which is assigned a radius, polarizability and a constant
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these parameters are derived from quantum mechanics and/or experiments.
The fundamental equations of this approach are the elastic force equation, different kind of
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2) What is the difference between an elastic force and an elastic potential? What is the connecting
element in molecular mechanics?

The elastic force is the force that an elastic body opposes when is deformed, analytically
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where k is the elasticity constant [N/mm], r is the final position of the body and b is the initial
(equilibrium) position.
The elastic potential is the energy of the body associated with the elastic force field, analytically
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In case of MM we consider two atoms (i and j), connected by a connecting element, which is
treated as an elastic body (rij: actual distance between atoms, bij: initial equilibrium distance).
The problem is to determine what is this element: from the Standard Model of Matter we know
that atoms are made by massive, point-like nuclei surrounded by tightly bound, rigid shells of
core electrons (atomic orbitals: s, p, d, f) and they are bounded together by valence electrons,
which form molecular orbitals, hence, molecular orbitals are the connecting elements between
two atoms1.

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3) What is the molecular mechanics parameterization? What is a force field? What are the
limitations of this approach?

Molecular orbitals in MM are parameterized by a force field, which consists of various analytical
expressions involving several parameter for each type of atom (atomic mass, van der Waals
radius, partial charge for individual atoms, equilibrium values of bonded atoms and effective
spring constant for each potential)2. Hence the connecting element between two atoms in
molecular dynamics is parameterized by a force field, namely an interaction model.
The limitations of this approach are that it requires extensive parameterization, the energy
estimates are not very accurate, it cannot be used to simulate reactions (broken/formed bonds)
and so it has limited abilities for providing accurate details regarding the chemical behaviour of
the system.

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4) What are the bond interactions among atom? What do they count for? Examples.

Bond interactions are one of the two terms of the force field used in classical molecular
dynamics simulation and they count for covalent bonds. There are four types of them:
Stretching between two atoms, represented by harmonic potential:
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Angle potential between a triplet of atoms, represented by harmonic potential:

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Proper dihedral angle (torsion) between two planes ([j, k, l] and [k, i, l]) containing four atoms:
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Improper dihedral angle (planar groups) between two planes containing four atoms:
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5) What are the non-bond interactions among atom? What do they count for? Examples.

Non-bond interactions are the second term of the force field used in classical molecular
dynamics simulation. There are two types of them:
Electrostatic potential (ions), Coulomb interaction between two charged particles:
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Van der Waals force, it is the sum of the attractive/repulsive forces between non-bonded and
neutral atoms. They include:
force between two permanent dipoles (Keesom force),
a permanent dipole and a corresponding induced dipole (Debye force)
two instantaneously induced dipoles (London dispersion force).
All these interactions are often taken into account only within a certain short distance from a
given particle (beyond this cut-off distance they are neglected for computational efficiency) and
they are usually included by a Lennard-Jones potential:
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6) How do we control system variables in molecular dynamics? What is a thermostat? What is a
barostat?

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atoms, obtaining the vector position and the vector velocity for each atom:

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A Verlet scheme is usually adopted for the numerical solution of these equations.
A thermostat is an algorithm used in MD simulation in order to control the simulation
temperature; the most used thermostats are:
Berendsen thermostat: an external heat bath with a fixed Tbath is coupled to the system; velocities
are scaled proportionally to Tbath ± T(t) such that the deviation exponentially decays with some
time constant IJ, which determines how tightly the bath and the system are coupled together
(usually IJ =0,4 ps).
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Nosè-Hoover ther mostat: equations of motions are changed by introducing a friction factor
proportional to particle velocity and friction coefficient ߦ, it induces temperature oscillations:
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A barostat is an algorithm used in MD simulation in order to control the simulation pressure; the
most used barostat is the Berendsen barostat, similar to the thermostat, an external bath with a
fixed Pbath is coupled to the system; velocities are scaled proportionally to Pbath ± P(t) such that
the deviation exponentially decays with some time constant IJP, which determines how tightly the
bath and the system are coupled together (usually IJP =1,0 ps).
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 7) Which are the essential steps for running a numerical simulation of molecular mechanics?

The essential steps for a numerical simulation of MM are:

a) Geometry generation: generate the geometry of the nano-tube that has to be simulated;
different formats are possible:
- *.xyz: provides the number of atoms, the type (label) and the coordinates in the matrix;
-*.pdb: provides the atoms coordinates list and the atom bonds list.
Force Field
applies hereb) Energy mini m ization: implement the force field and before starting the simulation find the
system configuration with minimum potential energy (i.e. depending on positions). This can
be very beneficial for the numerical convergence of the subsequent computations.
c) Thermal equilibration: bring the system in steady state equilibrium, all the atoms have the
same temperature of the environment. An index file must be obtained (MATLAB), which
provides the division of the atoms in sections.
d) Non-equilibrium simulation: couple the system with two thermostat at both ends, one at high
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file. Visualize the results (MATLAB).

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