Classic and Quantum Simulations of nano- and bio-systems
Basic Course
Lecturer
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
Introduction to molecular modelling, two-dimensional and three-dimensional models, available databases, molecular graphics
Protein structures and homology modelling, sequence alignment with BLAST, template identification, building a model
Molecular Mechanics, bonding and non-bonding terms, force-field parametrisation, parametrisation from ab-initio methods
Minimisation methods. First order methods. Second order methods. Choice of method
Molecular dynamics principles. The Verlet algortihm. Statistical ensambles. Monitoring equilibrium. Properties as statistical averages
Analysis of molecular dynamics trajectorie. Evaluation of thermodynamic parameters. Structural indicators. Graphical visualization of a trajectory
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
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