By combining the accuracy of quantum mechanics (QM) and the speed of molecular mechanics (MM) they enable studying specific properties beyond the reach of those methods in isolation (such as photochemical effects, ligand binding, reactivity, and a long et cetera). However, the preparation of such simulations can be difficult and tedious. Additionally, subtle changes in the setup process can often affect the accuracy and robustness of the results. This course aims to showcase a consistent protocol to set up your system in order to run QM/MM simulations using CP2K.
This course covers basic tools and technologies needed to succeed in setting up a QM/MM simulation with the AmberTools suite, and will be run with hands-on exercises. It provides a background to the preparation of biological systems for molecular modelling and offers practical experience in creating topologies successfully and running simple QM/MM simulations with CP2K in a HPC environment (ARCHER). You will learn about the intricacies behind the molecular modelling of biological systems, such as the practical skills required to handling and preparing PDB files to create ready-for-use topologies in CP2K.
At the end of this session you will be able to …
- Describe the main features of the AmberTools package
- Build topologies and coordinates ready to use in CP2K
- Run simple CP2K QM/MM simulations in a HPC environment
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 exercises.
The duration of the sessions will be between 2 and 3 hours, depending on the level of interactivity.
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 users, MobaXTerm or PuTTY work well, though other options are available 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)
Prerequisites
In this lesson we use AmberTools remotely on ARCHER. The following is expected:
- Comfortable using the Linux command line.
- Prior experience with HPC computing or QM/MM knowledge are not required.
This online course is a collaboration between ARCHER2 Training and BioExcel.