Intended
Audience:
A junior/senior level course for MAT and BIO majors, PHYS minors, or anyone
interested in understanding the microscopic basis of physically observed
phenomena using modeling and simulation.
Aims: To introduce various modeling techniques operative at
the atomistic and meso- time and length scales
relevant to the understanding of the structure-property relationships of
“materials” where a material is defined in the broad sense of anything that is
utilized for a particular human defined purpose; to introduce a conceptual
framework for the understanding of macroscopic observations of materials from a
microscopic viewpoint; to include modeling and simulation on equal footing with
experiments in attacking problems; to provide the background for choosing the
appropriate technique suited to the system at hand.
Instructor: Canan Atýlgan – office: 2058;
phone: 9523; e-mail: canan@sabanciuniv.edu
Assistant: Gökçe Güven – office: 2102;
phone: 2111; e-mail: gokceguven@sabanciuniv.edu
Hours: theory session – Wed 8:40
– 10:30 (L027); hands-on session – Wed 12:40 – 13:30 (G032)
Textbooks: Hinchliffe,
Molecular Modelling for Beginners 2nd ed. Wiley
(2008). ISBN: 978-0-470-51314-9
Frenkel & Smit,
Understanding Molecular Simulation 2nd ed. Academic Press (2002).
ISBN: 0-12-267351-4
Leach,
Molecular Modelling 2nd ed. Prentice Hall
(2001). ISBN: 0-582-38210-6
Course
Organization:,
hands-on sessions (1 hr/wk), structured instruction (2 hrs/wk), off-class assignments
Evaluation will be based two midterms (20
% each), assignments (50 %) and participation (10 %).
COURSE OUTLINE:
Week 1: The problem of time and length scales in molecular
modeling; coordinate systems; potential energy surfaces; molecular graphics.
Hands-on
session: Tutorial for molecular graphics programs
Aim: Introduce computational tools operative at
various time and length scales
Week 2: Introduction to all-atom methods; force
fields and their parameterization.
Hands-on
session: Defining NAMD coordinate and potential files
HW1: Molecule visualization
Aim: Learn how to choose a force field suitable for a
particular system of interest.
Week 3: Calculation of forces from energies for simple
potential functions.
Hands-on
session: Running sample MD programs in NAMD and seeing the results of bad
initial structures
Aim: First experience on the capabilities of molecular
simulation.
Week 4: Energy minimization; non-derivative, first- and
second-derivative methods. Degrees of freedom of a system.
Hands-on
session: Calculating internal coordinates using a molecular graphics programs
Aim: How and when to choose a minimization algorithm
suitable for a particular purpose.
Week 5: The Boltzmann distribution.
Hands-on
session: Calculating the averages and distributions of internal coordinates
HW2: Random number generation
Aim: See why the Boltzmann distribution is central to
molecular simulations.
Week 6: Introduction to conformational searching. Systematic and random search methods.
Hands-on
session: Distorting structures leads to new conformations!
HW3: Conformational search
Aim: Identify the different conformations of a
molecule.
Week 7: Normal
mode analysis and its relation to spectroscopy.
Hands-on session: NMA using 1-D and 2-D molecules.
HW4: NMA on a simple 4-atom 2-D molecule
Aim: Study the influence of conformations of a molecule on its
properties. Introduce a method for the direct comparison of experiment and
simulation.
____________________________________________________Spring
break
Week 8: Review for Midterm I and
Midterm I (Apr. 11)
Week 9: Monte Carlo simulations; importance sampling. Ergodicity.
Hands-on
session: Setting up a two dimensional simulation box for MC
simulations.
HW5: Monte Carlo Simulations of the
Ising Model
Aim: Implement the idea of a trajectory and pave the
way for the calculation of simple thermodynamic properties.
Week 10: General comments on “trajectory” methods; periodic
boundary conditions; some tricks for an efficient simulation.
Hands-on
session: Setting up a two dimensional simulation box for MC
simulations - continued.
Aim: Understand the capabilities and the limitations
of a dynamic simulation method based on first principles.
Week 11: Molecular dynamics simulations: Setting up.
Hands-on
session: Setting up an MD simulation.
HW6: Molecular Dynamics –
simulating miscibility of two liquids
Aim: Establish the fundamentals of a molecular
simulation.
Week 12: Molecular dynamics simulations: Prediction –
Thermodynamic properties, radial distribution functions (RDFs).
Hands-on
session: Analyzing an MD trajectory.
HW7: Molecular Dynamics – analyzing
the simulations (diffusion coefficients, RDFs, heat capacity)
Aim: Bridge theory and experiments based on the
dynamic simulations.
Week 13: Coarse graining: Dissipative
Particle Dynamics (DPD).
Hands-on
session: Setting up and analyzing a DPD simulation.
HW8: Dissipative Particle Dynamics
for a surfactant system
Aim: Assess limitations and benefits of simulating
larger systems.
Week 14: Review for Midterm II and
Midterm II (May 23)
SOFTWARE:
o Various molecular visualization software (e.g. Accelrys DS Visualizer, VMD: http://www.ks.uiuc.edu/Research/vmd/)
o Molecular Dynamics software
(NAMD: http://www.ks.uiuc.edu/Research/namd/; Materials Studio)
o Some programming of your own (nothing fancy – just
basic programming to analyze data you produce from the package programs above)