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Molecular Simulation

Code: Q3023     Acronym: Q3023     Level: 300

Keywords
Classification Keyword
OFICIAL Chemistry

Instance: 2021/2022 - 2S

Active? No
Responsible unit: Department of Chemistry and Biochemistry
Course/CS Responsible: Bachelor in Chemistry

Cycles of Study/Courses

Acronym No. of Students Study Plan Curricular Years Credits UCN Credits ECTS Contact hours Total Time
L:Q 0 study plan from 2016/17 3 - 6 56 162

Teaching language

Suitable for English-speaking students

Objectives

Relate macroscopic properties of gases and liquids with the description of the systems at the atomistic level.

Learning outcomes and competences

At the end of this course the student should be able to:

1- Relate macroscopic thermodynamic properties of liquids and gases to their atomistic behavior.

2- Discuss and distinguish the different limitations of applicability of Molecular Dynamics and Monte Carlo simulations.

3-Know how to launch computations based on these two methods and to interpret the results.

4- Know how to apply different simulation methods to study solute/solvent systems (e.g.: ions and small molecules in water) and and to study phase equilibrium of pure substances and mixtures

Working method

Presencial

Program

Theoretical topics:

  1. Introduction to Statistical Thermodynamics.
  2. Calculation of simple thermodynamic properties.
  3. Introduction to the Molecular Dynamics method (MD).
  4. Force Fields: the interaction between particles.
  5. Introduction to the Monte Carlo method (MC).

 

Practical applications:

1. Using GROMACS simulation program.
2. Using visualization programs / handling of MD results (VMD and Xmgrace).
3. Running simple simulations of gases and liquids; solvated ions in water and other solvents.
4. Molecular simulation for the direct study of phase equilibrium.
5. Simulations of isotherms of adsorption of gases in solid surfaces.

Mandatory literature

Hinchliffe Alan; Molecular modelling for beginners. ISBN: 9780470513149

Teaching methods and learning activities

Classes take place in a room equipped with video projector and computers/terminals (one per student).

Synchronization between presentation of theoretical topics and direct application on the computer by the students.

Individual practical works (computer simulations) which promote students' autonomy and discussion with colleagues and teacher, having as motivation the need to solve the problem in question.

Software

MCCCS Towhee
Gromacs

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation Weight (%)
Trabalho prático ou de projeto 50,00
Apresentação/discussão de um trabalho científico 20,00
Teste 30,00
Total: 100,00

Amount of time allocated to each course unit

designation Time (hours)
Estudo autónomo 56,00
Frequência das aulas 56,00
Trabalho laboratorial 50,00
Total: 162,00

Eligibility for exams

The students must attend at least 75% of the practical classes

Calculation formula of final grade

Final score = Oral presentation (20%)+ Test (30%) + Practical works (50%)

Special assessment (TE, DA, ...)

Working students and association leaders may opt for a practical assessment alternative that consists of making a practical work to be randomly chosen among those held during the semester and prepare its report.
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