Classic and Quantum Simulations of nano- and bio-systems

Basic Course

Lecturers:
Miguel Angel Soler Bastida, Paolo Giannozzi (University of Udine)

Board Contact:
Federico Fogolari, Paolo Giannozzi

SSD: FIS/03, FIS/07

CFU: (3 + 2) CFU

Period: February 20, 21, 22, 24, from 2.30 pm to 5.30 pm

Lessons / Hours: 12 hours

Program:

  1. Introduction to molecular modelling, two-dimensional and three-dimensional models, available databases, molecular graphics
  2. Protein structures and homology modelling, sequence alignment with BLAST, template identification, building a model
  3. Molecular Mechanics, bonding and non-bonding terms, force-field parametrisation, parametrisation from ab-initio methods
  4. Minimisation methods. First order methods. Second order methods. Choice of method
  5. Molecular dynamics principles. The Verlet algortihm. Statistical ensambles. Monitoring equilibrium. Properties as statistical averages
  6. Analysis of molecular dynamics trajectorie. Evaluation of thermodynamic parameters. Structural indicators. Graphical visualization of a trajectory
  7. Molecular dynamics simulations from first principles. Density functional theory. Plane waves and pseudopotentials methods. Fundamental state dynamics and Car-Parrinello dynamics

Verification: Practicals during the course and assignment

Prerequisites: None