This online course is a collaboration between ARCHER2 Training and BioExcel.
This online course consists of an interactive hands-on practical session presented remotely using Collaborate. Attendees will be given access to ARCHER to execute the practical.
The duration of the sessions will be between 2 and 3 hours, depending on the level of interactivity.
Overview:
QM/MM simulations enable researchers to model different biological processes at atomistic level and study specific properties that no other method can provide (such as photochemical effects, ligand binding, reactivity,…). Also they benefit from the accuracy of quantum mechanics (QM) and the speed of molecular mechanics (MM) methods. However, the preparation of such simulations are not easy and often subtle changes in the setup process can affect the validity of the results. This course aims to showcase how to run QM/MM simulations using CP2K.
This 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.
Learning outcomes:
- At the end of this session you will be able to…
- Describe the main features in the (of the?) AmberTools package
- Build topologies and coordinates ready to use in CP2K
- Run QM/MM simulations in a HPC environment
Audience:
- The course is aimed at biomolecular modellers who want to use QM/MM simulations in their work.
Prerequisites:
- Comfortable using the Linux command line
- Prior experience with HPC computing or QM/MM knowledge are not required.
Technical requirements:
- a microphone (webcam is optional) to take part
- Google Chrome or Firefox to access the session
- your laptop should have an SSH client (for window user Putty or any choice e.g. WDL) and a valid public SSH key.
- Access to AmberTools and CP2K will be provided on ARCHER
Trainers:
- Salome Llabres, EPCC
- Julien Sindt, EPCC
- Holly Judge, EPCC
- Arno Proeme, EPCC
Note: this session has been created in the context of the BioExcel remote training programme. This course is free to attend but we ask that you provide us with feedback after the training to help us optimise our training programme.
This course is now fully booked with a long waiting list.