Lecture 1

78648
Laboratory of
Molecular Design and
Materials Simulation
Chemical and
Process Engineering
 OUTLINE

•Instructor
•Course Schedule and organization
•Reference books
•Final exam
•Introduction to Molecular Dynamics
•Software used in the course: MAPS
•Applications of Molecular Simulations

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Contact

Instructor: Maria Grazia De Angelis, PhD, Associate

Professor in Chemical Engineering Principles
Email: grazia.deangelis@unibo.it
Phone: 051-2090410
Website: https://www.unibo.it/sitoweb/grazia.deangelis
FB: Mg Da
Office is located in Chemical Labs, Via Terracini 34 Google
street view

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Classes timetable and place

Place: LADI Computing LAB, DICAM, Ground Floor.

-If necessary, the students will be divided in groups.

-Attendance to classes is strongly suggested
- Slides will be provided.
-please join the mailing list for updated info on the Course
grazia.deangelis.Lab_Mol_Des_2018
-NO PREREQUISITES ARE NEEDED

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Reference books

1) Understanding Molecular Simulation, D. Frenkel, B. Smit.

2) Computer Simulation of Liquids, Allen, Tildesley.
3) Theory of Simple liquids, Hansen, Mc Donald.
 Final exam

1. For the exam, the student must prepare a report based on a

certain specific problem, selected in collaboration with the
Professor.
2. The report (5-20 pages) shall include a bibliographic review
on the topic using bibliographic resources available online at
UNIBO and an example of simulation carried out by the
student with the MAPS software.
3. Dates for the exam and presentation of the report will be set
by appointment.
 Software Installation

1. The students will install the software in their laptop through a

personal temporary license provided by the company, expiring in
July 2018. The license is permanently coupled to just one Computer
owned by the Student. It is important that the students prepare the
final project before the expiration date
2. To obtain their personal temporary license, the students shall
provide the MAC address of their PC (physical address of the
network card). How to find your MAC address:
https://kb.netgear.com/1005/How-to-find-a-MAC-address
3. MAPS can in principle run with Windows and Mac (Apple)
machines, but it is strongly suggested to use WINDOWS.
4. When you launch the program, you must be connected to the
Internet through the network card provided, so that the license will
be activated.
 Software Presentation

https://www.youtube.com/watch?v=FDvbfjxGeok
 Software Installation

1. The software contains different components, namely a simulation

engine (LAMMPS) plus the Amorphous Builder which generates
the initial structure. And the graphical interface to set up the
structure, the calculation parameters and analyze the results
2. Students must bring their own laptop during class so that they can
run the examples on their own according to the given instructions
 Different approaches to describe matter

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 A Different Type of Simulation

• Many Physically-Based
Simulations model
easily observable real
world phenomena.

• Molecular Dynamics
Simulations model
things too small for us
to observe directly.
 Why Not Quantum Mechanics?
• Modeling the motion of a complex molecule
by solving the wave functions of the various
subatomic particles would be accurate…

 22
   U ( x , y , z )  ( x , y , z )  E ( x , y , z )
2m
• But it would also be very hard to program
and take more computing power than
anyone has
 Classical Mechanics

• Instead of using Quantum mechanics, we

can use classical Newtonian mechanics
to model our system.
• This is a simplification of what is actually
going on, and is therefore less accurate.
• To alleviate this problem, we use
numbers derived from QM for the
constants in our classical equations.
 Molecular Modeling

For each atom in every molecule, we need:

• Position (r)
• Momentum (m v)
• Charge (q)
• Bond information (which atoms, bond
angles, etc.)
 From Potential to Movement
To run the simulation,
we need the force on Fi  mi a i
each particle.

We use the gradient of

the potential energy Fi   iV
function.
2
dV d ri
  mi 2
Now we can find the
acceleration.
dri dt
 What is the Potential?

A single atom will be affected by the potential

energy functions of every atom in the system:

• Bonded Neighbors
• Non-Bonded Atoms (either other atoms
in the same molecule, or atoms from
different molecules)

V ( R )  E bonded  E nonbonded
 Non-Bonded Atoms

There are two potential functions we need

to be concerned about between non-
bonded atoms:

• Van der Waals Potential

• Electrostatic Potential

E nonbonded  E van  der Waals  E electrostatic

 The van der Waals Potential

• Atoms with no net electrostatic charge

will still tend to attract each other at
short distances, as long as they don’t
get too close.
• Once the atoms are close enough to
have overlapping electron clouds, they
will repel each other with astounding
force
 The van der Waals Potential

One of the most widely used functions

for the van der Waals potential is the
Lennard-Jones. It is a compromise
between accuracy and computability.

 Aik C ik 
E Lennard  Jones    12  6 
nonbonded  rik rik 
pairs
 The van der Waals Potential
The Constants A and C
depend on the atom
types, and are derived
from experimental data.

 Aik Cik 
  12  6 
nonbonded  rik rik 
pairs
 The Electrostatic Potential

• Opposite Charges Attract

• Like Charges Repel
• The force of the attraction is inversely
proportional to the square of the
distance

qi qk
Eelectrostatic  
nonbonded Drik
pairs
 Coulomb’s Law

q1q2
F
4 0 r 2
 The Non-Bonded Potential

Combine the LJ and

Electrostatic Potentials

E nonbonded  E van  der Waals  E electrostatic

 Bonded Atoms
There are three types of
interaction between
bonded atoms:

• Stretching along the

bond
• Bending between bonds
• Rotating around bonds

E bonded  E bond  stretch  E anglebend  E rotate along bond

 Bond Length Potentials

Both the spring constant

and the ideal bond length
are dependent on the
atoms involved.

E bond  stretch  K
1, 2 pairs
b (b  b0 ) 2
 Bond Angle Potentials

The spring constant

and the ideal angle
are also dependent
on the chemical type
of the atoms.

E bond bend   K  (  
angles
0 ) 2
 Torsional Potentials

Described by a
dihedral angle and
coefficient of
symmetry (n=1,2,3),
around the middle
bond.

E rotate along bond   K  (1  cos( n ))

1, 4 pairs
Molecular Mechanics Force Fields
Example:
CFF (Consistent Force
Field)

•each of the terms has a physical meaning

that describes the change in total energy
caused by a change in a particular internal
coordinate /bond angle, torsional angle etc)
•There is a large number of parametersfrom
QM calculations or experimental data
 Link between different descriptions

The macroscopic variables are the average of microscopic

variables calculated over a large number of molecules
for a certain time interval
The link between micro and macro variables is given by
statistical mechanics :
– SM gives an interpretation of non mechanical
quantities such as U and S.
– SM gives a description of the system that is in
agreement with «classical» or «macroscopic»
thermodynamics.
CLASSICAL STATISTICAL

Averaging
P, T, V

3 variables to define
the state  1020 variables to
define the state
Some introductory
concepts of
STATISTICAL
MECHANICS
 Microscopic configurations: ENSEMBLES
• An ensemble is formed by a set of configurations (microscopic box formed
by N molecules, specified by 6N variables=3N coordinates (x,y,z)+3N
velocities (vx, vy, vz)) that all satisfy certain macroscopic constraints:
– NVE ensemble is formed by all possible configurations of N molecules with total
energy E and total volume V. (MICROCANONICAL ENSEMBLE)
– NVT ensemble is formed by all possible configurations of N molecules with
temperature T and total volume V. (CANONICAL ENSEMBLE)
– NPT ensemble is formed by all possible configurations of N molecules with
temperature T and pressure p.
- mVT ensemble is formed by all possible configurations of molecules with
chemical potential m, temperature T, total volume V. (N Not fixed) (GRAND
CANONICAL ENSEMBLE) useful for phase equilibria
• The several configurations belonging to a same ensemble are, in general,
not distributed evenly, i.e. they are not all equally probable.
 Probability functions

• Usually, the higher the energy of a certain configuration in

an ensemble, the lower its probability to occur.
• Therefore, in the microcanonical (NVE) ensemble, as all
configurations have all the same energy E, they all have the
same probability to occur.
• In the canonical ensemble the probability follows the energy
according to the Boltzmann distribution law
1
exp (- b E i )
PROBABILITY of configuration i in (NVT)= Q
With b Boltzmann constant=R/NA and Q proportionality
constant named partition function
Probability functions
 MOLECULAR DYNAMICS (MD)

Is a technique to compute the equilibrium and transport properties of

systems formed by many particles
The motion of the particles follows classical mechanics laws
(Newton’s) interacting with specific forces according to a FORCEFIELD

d 2 ri
Fi  mi ai  mi 2 ri = particle position
dt
Integration of Newton’s law for all particles gives us the positions and
velocities ri(t) and ri’(t) at each time for each particle i.
From such information, using Statistical Mechanics laws (averaging)
we obtain average macroscopic quantities as in a real experiment
MD is more similar to real experiments than MonteCarlo (the other
important molecular simulation technique)

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 MOLECULAR DYNAMICS (MD)
EXAMPLE: obtain temperature from a MD simulation output
At a microscopic level, temperature is related to total kinetic energy of
molecules:
mi vi  t 
2 N= number of particle in the system
N
T (t )   Nf=number of degrees of freedom of the system =3N-3 for
i 1 bNf a system with N particles and fixed total momentum
b=Boltzmann constant

vi=velocity of each particle

mi= mass of each particle
CLASSICAL STATISTICAL

Averaging
P, T, V
STATISTICAL
3 variables to define MECHANICS
the state  1020 variables to
define the state
431- 78648 Laboratory of Molecular Design and
Materials Simulation
 Force Fields implemented in LAMMPS

A force field has 2 parts: the formulas that define it and the coefficients used for a
particular system. Formulas implemented in LAMMPS correspond to formulas commonly
used in the
CHARMM (MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo,
Ha, et al, J Phys Chem, 102, 3586 (1998)
AMBER (Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell,
Kollman, JACS 117, 5179-5197 (1995).)
DREIDING force fields.
DREIDING is a generic force field developed by the Goddard group at Caltech and is
useful for predicting structures and dynamics of organic, biological and main-group
inorganic molecules.

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Analysis of MD trajectories
The evolution of a system in time during a molecular dynamics calculation is called
a trajectory.
Such a trajectory can be obtained by saving the coordinates and velocities of all
atoms in the simulated system at regular intervals.
This creates a massive amount of data, which is not easily understood.
Trajectories can be visualized using molecular graphics programs and a first visual
impression of the behavior of the system can be obtained this way.
However, it is often desirable to perform an analysis of the trajectory to focus
attention on specific features of the system.

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Software Used

Software used is MAPS® by Scienomics (commercial). It is a

MOLECULAR DYNAMICS (MD) software .
Software provides a graphical interface to build the
molecules and packing models, as well as a large database
for properties and parameters.
The ENGINE (integration of Newton’s laws of motion for the
molecules of the packing model) of the software is a freeware
one named LAMMPS (Large-scale Atomic/Molecular
Massively Parallel Simulator)
The software provides easy access to elaboration of
simulated data to obtain macroscopic quantities and visualize
with graphs.
431- 78648 Laboratory of Molecular Design and
Materials Simulation
 Where to find tutorials

Building molecules
MAPS Manual\Tutorials\Fast Track Tutorials
LAMMPS
MAPS Manual\Tutorials\LAMMPS
 Manual-1
1.1. Sketching tools to quickly create 3D molecular models
In the viewer, you can enable or disable the Sketch toolbar:

Add atom: select the build item you need (atom or group) and click the
atom to which the build item should be attached to

Sketcher select the element you want to sketch with, click on the sketching
tool and start drawing the system of interest.

Add hydrogens: in a structure containing hydrogen atoms, you can sketch

everything with the standard sketching tools. At the end you can add the
hydrogen atoms missing by a simple click on the add hydrogens button.
 Manual-2
Delete atom/group: select this button and then click on the atom you want to delete. In
case you have selected more than one atoms, it deletes all selected atoms (group).

Delete hydrogens: this option reverses the action of the add hydrogens button. It
removes all hydrogen atoms added by clicking on the add hydrogens button.

Replace atom: modifies the system by replacing one atom with another atom or
group. Select the build item you want to introduce and click on the atom you want to
replace.

Connect fragments: connect 2 fragments by creating a bond between the atoms

selected. The bond length and number of hydrogen atoms are automatically adjusted. If two
atoms are selected each of these atoms has to be connected to exactly one hydrogen atom.
The bonds between the atoms selected and the hydrogen atoms are aligned and the fragment
which contains the atom selected as the second one is rotated into the appropriate
orientation. If one or both of the atoms selected are connected to more than one hydrogen
atom one hydrogen atom needs to be selected as well for each atom to determine the bonds
to align.
 Manual-3
Fuse fragment: fuse two fragments by overlaying two bonds. The number of
hydrogen atoms is automatically adjusted. Select two bonded atoms in one
fragment, then select two bonded atoms in the other fragment, then press this
button to fuse the fragments.

Invert stereo chemistry of atom: invert stereo chemistry of atom changes the
conformation of a stereo center from S to R or vice versa if the atom selected is a
chiral atom.

Change geometry: modify bond distances, bond angles, or torsion angles

interactively.

Move group : selecting this enables you to perform rotations and translations
on a part of the molecule. Unselecting this switches back to the full mode where
the whole system is rotated and/or translated.
 Manual-4
Modify cell: opens a dialog for modifying cells, create supercells or remove
symmetry (make P1 symmetry). A click on this button opens the Unit cell dialog.

Clean structure: allows you to quickly optimize the structure of the system
sketched using the Universal Force Field (UFF)
Warning : this is not a very reliable method and thus a proper optimization
procedure should be used.

Fix atoms: allows you to fix atom. Click on this icon to open the corresponding
dialog (displayed below). In this dialog you can either select to fix atomic position.

Assign force field: this button calls the Assign force field dialog which allows
you define the force field to be used in a classical simulation i.e., geometry
optimization or molecular dynamics.
 Manual-5
Build item: select the atom or group which should be added when
the Add Atom/group button is active and an atom is clicked at in the model
viewer. The list can be modified by selecting the last item (Edit list). Selecting
this item opens the Select building item dialog.
Note : you can create your own fragments by drawing and saving them as *.cml
file in the groups folder of MAPS. Please see Saving a model as template.

Torsion angle: select the torsion angle to apply when groups are added
in the model viewer.
 Manual-Amorphous builder 1
Input
Composition table: in this table you can specify the composition of the amorphous system to be build.
Each row corresponds to one component of the system. In the Project column choose the project in
which the model you want to use is located. In the Molecule column select the model.
Use Number column to specify the number of molecules for the corresponding component. Changing the
number of molecules for a component the Density will be updated. Use Add and Delete buttons located
at the right of this table, in order to add or delete components.
Matrix model: check this check box to use a model as a starting point for the amorphous system growth.
The adjacent combo boxes select model you want to use (first the project where the model is located and
the actual model).
a, b, c, α, β, γ: cell parameters. Changing any one of these parameters, the Volume and the Density will
be updated.
Temperature [K]: specifies the temperature for constructing the amorphous system.
Density [g/cm3]: specifies the target density for the amorphous system to be build. The density will be
used to construct a box containing the amorphous system. Box edges will be adjusted in a affine way and
the Volume will be updated.
Volume [Å3]: specifies the volume for the amorphous system to be built. The volume will will be used to
construct a box containing the amorphous system. Box edges will be adjusted in a affine way and
the Density will be updated.
Seed for random number generator: specifies the seed for the random number generator.
 Manual-Amorphous builder 2
Options
Use threads: this option allows you to continue working with MAPS whilst the amorphous system is under
construction. This is useful, especially in the cases of large systems.
Use flexible bonds and angles: check this check box to use flexible bonds and bond angles during the
construction of an amorphous system. If this check box is not checked, bonds and angles will be set to
their equilibrium values.
Insert simultaneously: check this check box to grow all the molecules simultaneously in the simulation's
box. If this box is not checked the molecules will be inserted one at a time. This will result in a different
conformation.
Lateral atoms at the end: check this check box to insert lateral atoms (e.g. H) after the insertion of the
backbone of the molecule. If this check box is not checked, lateral atoms will be inserted in the simulation
box, after the insertion of the backbone atom on which they are attached.
Create a new project: check this check box to create a new project for the amorphous system. If this
check box is not checked, the amorphous system will be created in the same project as the model
corresponding to the first component.
Use non bonded interactions: check this check box to include non bonded interactions in the calculation
of systems' energy. If this check box is not checked, non bonded interactions will be excluded from energy
calculations. In this case, only hard sphere overlap and concatenation checks will affect the insertion of
molecules in the simulation box.
Build trials: specifies the maximum number of trials (bt) for the growth of a molecule in the simulation
box. Depending on the value of the back steps, it is possible to "recoil back" all the already inserted
particles of a molecule during the growth procedure of the molecule. This is considered a failed build
trial.Note: bt ≥ 1. Proposed value: bt ≤ 20.
 Manual-Amorphous builder 3
Insertion trials: Specifies the number of trials (nt) for the insertion of the first particle of a molecule in the
simulation box.Note: nt ≥ 1. Proposed value: nt ≥ 50.
Single step trials: specifies the maximum number of positions (np) that a particle can try in a recoil
growth insertion step.Note: np ≥ 1. Proposed value: 8 ≤ np ≤ 20.
Back steps: specifies the maximum number of particles (np) that can be "recoiled back" in order to
escape from a trap during the recoil growth procedure.Note: 0 ≤ np ≤ number of molecule's particles.
Proposed value: 2 ≤ np ≤ 5.
Scale groups: specifies the scale factor (sf) for the group size. Change this in order to avoid
concatenations during the first steps of minimization (after building the amorphous system).Note: If np ≥ 1
and if sf = 1.0 no scaling is performed. Proposed value: 1.0 ≤ sf ≤ 2.0.
Scale lateral bonds: specifies the scale factor (sf) for the bond lengths of atoms that are attached to a
group and have only one bond (e.g., hydrogen atoms).Note: 0.1 ≤ sf ≤ 1.0. If sf = 1.0 no scaling is
performed.
Scale hard sphere: Specifies the scale factor (sf) for the hard sphere overlap check.Note: 0.0 ≤ sf ≤ 2.0.
If sf = 1.0 no scaling is performed. Proposed values: 0.5 ≤ sf ≤ 0.6.
2D periodic: check this check box to remove periodicity on Z direction (2D periodic boundary conditions).
Confine in z direction: check this check box to convert cell z planes to impenetrable walls. In this way,
the system is confined between the two planes (sandwich). The adjacent speed boxes define the position
of the confine planes.
 Manual-Amorphous builder 3
low plane offset: use this spin box to change the offset of the low confine plane in z direction. The low
plane should always remains below the high plane.
high plane offset: use this spin box to change the offset of the high confine plane in z direction. The high
plane should always remains above the low plane.
Graft molecules: check this check box to graft the inserted molecule on z low/high confine plane.
on low plane: use this spin box to change the number of molecule grafted on the low confine plane. If
atoms belong to GRAFT_POINTS group exist in the matrix model and they are located below the low
plane, the graft point will be the projection of these atoms on the low plane. In a different case the graft
point will be selected randomly on the low plane.
on high plane: use this spin box to change the number of molecule grafted on the high confine plane. If
atoms belong to GRAFT_POINTS group exist in the matrix model and they are located abode the high
plane, the graft point will be the projection of these atoms on the high plane. In a different case the graft
point will be selected randomly on the high plane.
 Software Used

Build the model with AMORPHOUS BUILDER

E.g. box with 500 water molecules

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Software Used examples
Example: Modeling LIQUID WATER. Diffusivity, pressure
https://www.youtube.com/watch?v=FDvbfjxGeok

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Software Used examples
Example: Modeling Methanol, organometallic structure, polymer .
https://www.youtube.com/watch?v=_ADzxSzgQCw

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Software Used examples
Example: Modeling complex systems
https://www.youtube.com/watch?v=tCcAVttrPFI

431- 78648 Laboratory of Molecular Design and

Materials Simulation
 Applications of Mol. Sim.
From Last Annual AICHE meeting, some presentations on mol. sim.

Prediction of THERMODYNAMIC PROPERTIES :

-Force Field Assessment for Predicting Vapor-Liquid Equilibrium of Water in Ionic Liquids
- Accurate Calculations of Partition Coefficients with Atomistic Simulation Methods
- Molecular Dynamics Simulations of Structure-Property Relationships of Tween® 80 in Water and at
Interfaces
- Vapor-Liquid Coexistence Data for p-Cymene Using Equation of State Methods and Monte Carlo
Simulations
PHARMACEUTICAL APPLICATIONS
- Computational Screening of Cellulosic Excipients for Drug Delivery
MATERIALS SCIENCE:
- Atomistic Simulations of Structure and Mechanical Behavior of Primed and Unprimed Epoxy-Alumina
Interfaces
MODELING INDUSTRIAL SEPARATION PROCESSES (ADSORPTION)
-Applications of DFT Derived Force Fields for Olefin/ Paraffin Separation in MOFs
-Computational Screening of Metal-Organic Frameworks for Hexane Isomer Separation
MODELING POLYMER PROCESSING:
- Application of Molecular Simulations: Molecular Understanding of Electrospinning

431- 78648 Laboratory of Molecular Design and

Materials Simulation