Learning pathway

Using HPC infrastructure to perform biomolecular simulations

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Learning pathway written by:

  • Julien Sindt
  • Alessandra Villa
  • Marta Lloret Llinares


competency [at] ebi.ac.uk

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How to use the Linux command line and how to access an HPC infrastructure and run biomolecular simulation software on it

Guang is starting a PhD to study the mutations of a dopamine receptor through computational simulations. Following a master's project centred in wet lab experiments, Guang is now moving into computational biology. Guang has a strong background in chemistry and biology, but a limited familiarity with linux and supercomputers, which will be essential to run the simulations of the dopamine receptor.


Following this pathway, you can learn about the Bourne Again Shell (bash), Slurm workload manager, and ARCHER2 architecture. The aim is to give you an indication of the level of complexity of the computational techniques and knowledge required to run on a national high-performance computing facility. Parts of the pathway focus specifically on ARCHER2.

General outcomes

After going through this learning pathway you should be able to:

  • Use the Linux command line
  • Use Slurm Workload Manager
  • Describe the ARCHER2 architecture
  • Run jobs in ARCHER2


There are no prerequisites for this learning pathway.

If you are a Windows user, we recommend you use MobaXTerm (https://mobaxterm.mobatek.net/) to try the exercises in this course as this is also the recommended application for using ARCHER2.