Tutorial 04 - Add support for SOMD2 as a FEP engine

[akalpokas]

This PR adds support for using SOMD2 as a FEP engine for RBFE TYK2 tutorial. Users can pick SOMD2 as an engine from the dropdown menu in the jupyter notebook, and the added logic in the scripts handle SOMD2 input file and the configuration file creation.

I have tested the code to make sure there are no breaking changes introduced. These are the versions of code that I have tested which successfully handled input file creation and the FEP code running:

For SOMD the following versions work:

• BioSimSpace - 2023.3.1, 2024.1.0.dev0 (commit 4817660) [for input file creation]
• pmemd.cuda 2022.0 [for equilibration]
• Sire - 2023.3.2, 2024.1.0.dev0 (commit 4ccbb9f) [for running FEP code]

For SOMD2 (commit 5886dc) the following versions work:

• BioSimSpace - 2023.3.1, 2024.1.0.dev0 (commit 4817660) [for input file creation]
• pmemd.cuda 2022.0 [for equilibration]
• Sire - 2024.1.0.dev0 (commit 4ccbb9f) [for running FEP code] (the older version of sire could not run the FEP code, as this version of SOMD2 is calling sire.options attribute, which is not implemented until 2023.5 sire release)

I'm happy to do more tests or make any changes if needed.

[lohedges]

Thanks, this is great. I've only tested the setup part, so assume the SLURM scripts work based on your feedback. (The changes to the scripts look fine, though.)

My only question is whether we want to add any information to let the user know how to install `somd2?. Currently this isn't a BioSimSpace dependency, so would need to be installed separately. Other tutorials detail how to install additional tools that are required for the notebooks, perhaps we could add a similar note here?

Cheers.

[jmichel80]

I would keep the somd2 backend undocumented for now, as I don't think we want external users to start working with the code at this point.