08-10-2022

ME F315 Advanced Manufacturing Process

Introduction to Molecular Dynamics

BITS Pilani Dr. Radha Raman Mishra

Pilani Campus
Mr. Ayush Khaitan

Why do we do Simulation?

▪ In some cases, experiment is

• Impossible
• Too dangerous
• Expensive
• Blind

▪ It’s a very useful complement as

it can
• Replace Experiment
• Provoke Experiment
• Explain Experiment
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Kinds of Simulation

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Kind of Simulation
▪ Quantum Mechanics (QM)/Ab-
initio/DFT
• Electronic Structure (Schrodinger)
• Accurate, but extremely expensive
• For smaller systems

▪ Molecular Mechanics /Molecular

Dynamics
• Empirical forces (Newton)
• Less accurate, but practically fast
• Can be used for macromolecular
systems

▪ Mixed Quantum/Classical (QM/MM)

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Molecular Dynamics
▪ Molecular dynamics simulations calculate the motion of the
atoms in a molecular assembly using Newtonian dynamics to
determine the net force and acceleration experienced by each
atom. Each atom i at position ri, is treated as a point with a mass
mi and a fixed charge qi.

▪ Quantitative and/or Qualitative information about macroscopic

behavior of macromolecules can be obtained from simulation of a
system at atomistic level.
▪ Macroscopic properties are often determined by Molecule-level
behavior

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Molecular Dynamics

▪ Molecular Dynamics Process:

• Particles and atoms have potential energies from interaction and
bonding with other atoms, this energy can be descried by a
mathematical function called energy function:

• In Classical Mechanics, the Forces on atoms can be calculated if

we knew the potential energies of these atoms

• From Newton's Law

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Molecular Dynamics
▪ Molecular Dynamics Process:
• So we determine the trajectory and motion of the atoms by using
the following expression.

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Energy Functions: Interatomic

Potentials
▪ Empirical Potential Functions:
Assume a functional form for the potential function and then choose the
parameters to reproduce a set of experimental data. (Leonard-Jones,
Morse, Born-Mayer, Bond Order Potentials by Tersoff and Brenner)

▪ Semi-Empirical Potential Functions:

Derived from Quantum-Mechanical arguments, One can calculate the
electronic wavefunction for fixed atomic positions. This is difficult for a
system of many atoms. (Embedded Atom Method (EAM))

▪ Ab-initio:
One can perform direct electronic-structure (quantum-mechanics-based)
calculations of forces during so-called Ab-Initio Molecular Dynamics
(AIMD) simulation.

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Energy Functions: Pair

Potentials
▪ Pair potentials are the simplest form of a potential, that considers
only the two-atom interactions, and ignores the rest

▪ There are (N – 1) interactions per atom, and thus the number of

pairs, N pair, is on the order of N2:

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Pair Potentials: Leonard –

Jones Potential
▪ Leonard – Jones (1924): are the simplest form of a potential, that
considers only the two-atom interactions, and ignores the rest

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Pair Potentials: Leonard –

Jones Potential
▪ This simple pair potential can express the atomic interactions of
noble gases (Ne, Ar, Kr, etc.), spherical molecules, and secondary
bonds very well

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Energy Functions: Embedded

Atom Method (EAM)
▪ In metals and transition metals, atoms (or ions) are in the middle of
the electron sea and mostly coordinated with 8–12 other atoms.
▪ The coulomb interactions between them are long-ranged ones,
covering easily tens of atoms.
▪ The embedded atom method (EAM) considers the effective
electron density at a given atomic site as one of the parameters,
thereby capturing some electronic effects while maintaining the
simplicity of a potential.

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Energy Functions: Embedded

Atom Method (EAM)
▪ The EAM considers both contributions from the pair potential and
the embedding energy that approximates the missing N-atom
effect in a pair potential

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Energy Functions: Embedded

Atom Method (EAM)
▪ This type of potential works very well for most metals and transition
metals, especially for FCC metals.
▪ Does not work very well for Alloys

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Energy Functions: Bond

Order Potentials
▪ In covalent solids, deviations from the scheme of pairwise additives
are even larger since these solids are less closely-packed (often
with a coordination number of only 4) and have strong directional
bonds of equivalent strength.
▪ Bond angle and Bond order are the prime characteristics of these
materials, and the strength of a bond between two atoms depends
on the local environment such as coordination number and bond
angle.

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Energy Functions: Tersoff

Potential
▪ Tersoff Potential is one of the potentials which includes extra
geometrical and bond order related terms

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Energy Functions: Forcefields

▪ Force field potentials are designed for organics, polymers, and
bioorganic systems (for example, proteins)
▪ The forcefield is a collection of equations and associated
constants designed to reproduce molecular geometry and selected
properties of tested structures

▪ It used too describe the time evolution of

• Bond lengths
• Bond angles and torsions
• Van der Waals Interactions
• Electrostatic interactions

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Energy Terms in Forcefields

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Forcefields
▪ Examples on different
forcefields:
• AMBER
• CHARMM
• GROMOS
• OPLS
• MMFF

▪ All vary in:

• Functional Form
• Empirical Parameters
• Simulations Target

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Numerical Integration: Finding

Trajectories
▪ Newton’s equation represents a set of N second order differential
equations
▪ It’s impossible to solve this set of equations exactly to obtain the
trajectories of atoms
▪ We solve these equations Numerically at discrete time steps to
determine the trajectory of each atom.

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Numerical Integration: Verlet

Algorithm
▪ There are several algorithms available for the numerical integration
of Newton’s equations of motion and calculation of atomic
trajectories in practical MD runs:
• Verlet Algorithm (1967): Taylor expansion for forward and
backward positions in time

• Summing these two equations

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Numerical Integration:
VelocityVerlet Algorithm
▪ The velocity Verlet algorithm (Verlet 1968) is one of the most
frequently implemented methods in MD

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Timesteps
▪ We need to determine the timestep of the numerical integration of
the simulations trajectories, in which every unit of this time step we
do the integration
▪ The Timestep of MD simulations is limited by the event which has
the smallest time (Why!!)

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Timesteps: 1 fs barrier
▪ Atoms in a solid lattice vibrate in the range of 10−14

▪ Ideally the timestep should be 1/10 highest frequency (1/10×10−14s

= 1 femtosecond)

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Molecular Dynamics
Ensembles
▪ In a simulation box of an MD run, each atom moves and behaves
differently, and a new microstate of the system is generated in
every timestep
▪ An ensemble is the collection of possible systems that belongs to
the different microscopic states but with an identical macroscopic
or thermodynamic state.

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Molecular Dynamics
Ensembles
▪ As with actual experiments in a lab, we impose these external
constraints on ensembles to have particular properties out after a
run.
▪ Thermodynamic properties such as entropy S, Helmholtz free
energy F, Gibbs free energy G, and the chemical potential μ can
be derived from data obtained from these prearranged ensembles

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Periodic Boundary Conditions

▪ Periodic boundary condition (PBCs) are a set of boundary conditions
which are often chosen for approximating a large (infinite) system by
using a small part called a unit cell. PBCs are often used in computer
simulations and mathematical models.
▪ A “real” system might contain about NA = 6 × 1023 molecules. Simulation
may contain about 100-1,000,000 molecules. A small cube of 10x10x10
molecules has about half of the molecules on the Surface, this is Not
appropriate to study “bulk” properties
▪ PBCs have the following properties:
• Small box replicated in all directions
• A particle that leaves the box on one side is
replaced by an image particle that enters from the
other side
• There are no walls and no surface particles
• Actual simulation takes place only for the atoms
inside the primary
box at the center, and all image boxes just copy the
primary box.

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Minimization
▪ Minimization is a procedure that attempts to minimize the potential
energy of the system to the lowest possible point.

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Minimization: Steepest
Descent
▪ Steepest Descent is a method for obtaining local stationary points of a
multi-dimensional function
• X0 initial structure
• Compute U(R) and ∇𝑈(𝑅) Energy and Gradient
• Update Xi+1= Xi - γi ∇𝑈(𝑅) Displacement
• Check for Convergence
if Yes: Done Xf = Xi
if No: Return to step 2

▪ Convergence Check:

• | ∇𝑈 𝑅 | ≈ 0 Gradient
• | 𝑈 𝑥𝑖 − 𝑈(𝑥𝑖−1) | ≈ 0 Energy
• |𝑥𝑖 − 𝑥𝑖−1| ≈ 0 Displacement
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Minimization: Conjugate
Gradient
▪ Conjugate Gradient is a more advanced energy minimization
algorithm than steepest descent. It uses step history to accelerate
convergence

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MD Algorithm
1. Assign initial

2. Compute

3. Update

4. Update

5. Repeat until

6. Compute Desired
Properties

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Limitations of MD
▪ Timescales: Require shorter timesteps for numerical stability
• Usually 1 fs (1 × 10-15s)

▪ Timescales: Structural changes in protein can take up to

nanoseconds, microseconds, milliseconds or even seconds
• Requires millions, trillions or even more time steps, and thus
calculations

▪ Energy Functions accuracy: inherently, they are approximations

▪ No Electricity or Magnetism or Optical properties in Classical

MD

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Aims of MD simulation studies

▪ Understanding the properties of assemblies of molecules in terms
of their structure and the microscopic interactions between them
• Serves as a complement to conventional experiments, enabling us
to learn something new, something that cannot be found out in
other ways, …
▪ Bridge between microscopic length and time scales and the
macroscopic world of the laboratory
▪ Provides a guess at the interactions and “exact” predictions of bulk
properties
▪ Revealing hidden details of the bulk measurements
• E.g. Link between diffusion coefficient and velocity autocorrelation
function

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Software Tools for MDS

▪ Multiple Software packages are available for MD Simulations
• AMBER, NAMD, GROMACS, Desmond, Desmond-GPU
(Shrodinger), ACEMD (HTMD), OpenMM, CHARMM, LAMMPS
• Core functionality is same, force fields are compatible
• Differ in speed, scalability, cost and feasibility
▪ Visualization Tool: VMD , OVITO, Avogadro, and VESTA

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What can we study with MD

Simulations
▪ Since the time the MD method was introduced, it has been used to
investigate a wide range of problems in different research fields:
• Chemistry and Biochemistry: molecular structures, reactions,
drug design, vibrational relaxation and energy transfer, structure of
membranes, dynamics of large biomolecules, protein folding, …
• Statistical Mechanics and Physics: theory of liquids, correlated
many-body motion, properties of statistical ensembles, structure
and properties of small clusters, phase transitions..
• Materials Science: point, linear, and planar defects in crystals and
their interactions, microscopic mechanisms of fracture, surface
reconstruction, melting and faceting, film growth, friction, …

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What can we study with MD

Simulations

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THANK YOU
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