Preparing to run biomolecular QM/MM simulations with CP2K using AmberTools Online


Date: 9 June 2020
Time: 13:00 – 16:00 BST

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.

At the end of this session you will be able to:

  • Describe the main features in the AmberTools package
  • Build topologies and coordinates ready to use in CP2K
  • Run QM/MM simulations in a HPC environment

Places are strictly limited so please register to secure your place.

For more information on course perquisites and registration, please visit the ARCHER website.


Date/Time
09 Jun, 2020
12:00 - 15:00

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