Course content

To see details about the live BioExcel course on Biomolecular Simulations and the original programme, you can refer to the course page and programme.

The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainers
	Docking and HADDOCK
	Docking basics	Alexandre Bonvin
	Tutorial – HADDOCK	Alexandre Bonvin
	Molecular Dynamics Simulations with GROMACS
	Basis of molecular dynamics simulations	Alessandra Villa
	Tutorial – A guide to perform MD simulation with GROMACS	Alessandra Villa
	Short talk – Getting good performance in GROMACS	Berk Hess
	Simulation workflows with BioBB
	Computational biomolecular simulation workflows using BioBB	Adam Hospital
	Tutorial – Protein-Complex MD Setup with Jupyter Notebooks and BioBB.	Adam Hospital and BioBB
	QM/MM
	Introduction to QM/MM	Emiliano Ippoliti
	Tutorial – Introduction to QM/MM simulations using GROMACS-CP2K interface	Dmitry Morozov
	Enhanced-sampling methods
	Modeling molecular recognition through enhanced-sampling methods	Attilio Vargiu
	Tutorial – metadynamics	Giuliano Malloci, Attilio Vargiu, and Andrea Basciu
	Free energy calculations
	Introduction to alchemical free energy calculations using PMX	Bert de Groot
	Applications of alchemical free energy calculations	Vytautas Gapsys