LFU:online

The course aims at providing the practical tools to define, implement and carry out simulations in computational biophysics, employing professional open source software packages.

Part 1. Analysis of MD simulations: estimates and errors (theory).

Part 2. Molecular visualization: introduction to VMD and Pymol (2 hands-on sessions).

Part 3. Computational chemistry and force field parametrization (3 hands-on sessions).

Part 4. MD integrators: introduction to NAMD and applications (3 hands-on sessions).

Part 5. Coarse grained models (2 hands-on sessions) .

-       Mark E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford Graduate Texts.

-       Daan Frenkel and Berend Smit, Understanding Molecular Simulation, Academic Press.

-       M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Oxford Science Publications.

The students are supposed to be familiar wthi programming languages (at least one among C/C++, Fortran, Python), with the Linux operative system and with file system operations, in general.

The class is joint lecture with the University of Trento. The class consists of lectures as well practical lab classes where the students implement and run their computer programs. There will be a three-day retreat to Trento with lectures and lab classes which are fully funded by the Euregio program UNITN-UIBK.

For further information please contact Prof. Franosch