2024
Molecular Simulation
Name: Molecular Simulation
Code: QUI01109L
6 ECTS
Duration: 15 weeks/156 hours
Scientific Area:
Chemistry
Teaching languages: Portuguese
Languages of tutoring support: Portuguese
Sustainable Development Goals
Learning Goals
The objective of this unit is to give a broad view on the techniques of molecular simulations and on how these techniques can help to elucidate the structure of molecules as well as to predict some of their properties. In this regard, it is aimed to introduce the student with the basis of statistical thermodynamics, as well as with the tools to calculate macroscopic thermodynamic properties from spectroscopic information. It is also aimed to provide the student with the fundamental concepts and theoretical foundations underlying the simulation techniques as well as make him familiar with some of the most important algorithms used in this field.
Contents
Statistical thermodynamics: distribution of molecular states, partition functions, fundamental relationships, applications to the calculation of thermodynamic properties and chemical equilibrium.
Introduction to the molecular simulations. Periodic boundary conditions. Trajectories and properties. Ergodicity.
The Molecular Dynamics method. Simulations in the microcanonical ensemble. Simulations in the canonical ensemble: the Nosé-Hoover and the Berendsen thermostats. Simulations in the isobaric ensemble: the Berendsen and the Parrinello-Rahman barostats.
The Monte Carlo method. Canonical ensemble, isothermal-isobaric ensemble, grand canonical ensemble and Gibbs ensemble.
Analysis of simulations results. Radial distribution functions. Mechanical properties. Fluctuations. Correlation functions. Dynamical properties.
Introduction to the molecular simulations. Periodic boundary conditions. Trajectories and properties. Ergodicity.
The Molecular Dynamics method. Simulations in the microcanonical ensemble. Simulations in the canonical ensemble: the Nosé-Hoover and the Berendsen thermostats. Simulations in the isobaric ensemble: the Berendsen and the Parrinello-Rahman barostats.
The Monte Carlo method. Canonical ensemble, isothermal-isobaric ensemble, grand canonical ensemble and Gibbs ensemble.
Analysis of simulations results. Radial distribution functions. Mechanical properties. Fluctuations. Correlation functions. Dynamical properties.
Teaching Methods
The teaching / learning is based in the individual work of students, supported by recommended bibliography and notes taken by the students either during classes or through individual research. In the lectures the theory will be exposed, commented and discussed with the students. In practical classes, the subjects developed in the lectures are illustrated with problems of practical examples.
The evaluation, in the continuous regime, is carried out by the realization of 2 tests, one for the first half of the semester and the other for the second half, with equal weights of 50%. In the examination regime, the student accomplishes a single evaluation test (weight of 100% in the evaluation).
The evaluation, in the continuous regime, is carried out by the realization of 2 tests, one for the first half of the semester and the other for the second half, with equal weights of 50%. In the examination regime, the student accomplishes a single evaluation test (weight of 100% in the evaluation).
Teaching Staff (2023/2024 )
