This online course covers basic tools and technologies needed to succeed in the setting up a QM/MM simulation with AmberTools suite, with hands-on exercises. It provides background to preparation of biological systems for molecular modelling and practical experience in successfully creating topologies and running simple QM/MM simulations using CP2K in a HPC environment.

The course uses examples drawn from EPCC’s experiences in the life-sciences and HPC computing, but using free tools and technologies commonly used in the biomolecular modelling community. You will learn the intricacies of molecular modelling of biological systems, as well as practical aspects of handling and preparing PDB files, creating topologies ready to run using CP2K softwares.

Audience: The course is aimed at biomolecular modellers who want to use QM/MM simulations in their work.