Molecular Simulation

Code:

Q3023

Acronym:

Q3023

Level:

300

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2020/2021 - 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.

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:

Using GROMACS simulation program and visualization programs / handling of MD results (VMD and Xmgrace).

Using MCCCS Towhee simulation program.

Practical works: running simple simulations of gases and liquids; solvated ions in water and other solvents; more complex systems like biomolecules and, in particular, proteins

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 (%)
Prova oral	20,00
Trabalho escrito	30,00
Trabalho prático ou de projeto	50,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Apresentação/discussão de um trabalho científico	10,00
Estudo autónomo	4,00
Trabalho escrito	14,00
Trabalho laboratorial	28,00
Total:	56,00

Eligibility for exams

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

Calculation formula of final grade

Nota Final = Prova oral (20%)+Trabalho escrito(30%)+Trabalhos práticos(50%)