Fixes for steered MD tutorial and update to RBFE tutorial

[mb2055]

This brings the tutorials in line with the latest version of BioSimSpace.
Changes are in two places:

1. 04_FEP/02_RBFE - Now able to use the latest version of Cinnabar (also retains support for older versions). @annamherz I wasn't sure if there was a specific reason why cinnabar 0.3.0 was the one used, so I made sure the notebook still supports this version, but also later versions.
2. 03_steered_md - There had been some changes to the API and the tutorial was out of date. @lohedges I wasn't completely sure about the best choices for align_selection and rmsd_selection so I chose the same region for both, if there's a better choice here its easy to change.

[annamherz]

1. 4_FEP/02_RBFE - Now able to use the latest version of Cinnabar (also retains support for older versions). @annamherz I wasn't sure if there was a specific reason why cinnabar 0.3.0 was the one used, so I made sure the notebook still supports this version, but also later versions.

Hi! From what I recall, there wasn't a specific reason, mainly that the analysis was stable with that version at the time of writing 😄

[lohedges]

Just to note that the updated steered molecular dynamics tutorial requires an update to an input file within the data archive. Since these aren't versioned, I suggest creating a new archive on SharePoint, e..g data2.tar.bz2, then downloading it to the same archive name within the download script, i.e. data.tar.bz2. That way we don't break backwards compatibility for old versions of the tutorial.

@jmichel80: This file needs to replace reference.pdb in the data.tar.bz2 archive. The SharePoint link appears to be from your account, so it would probably be easiest if edit this. I suggest doing:

1. Download and upack the archive.
2. Replace the reference.pdb file with the one posted here.
3. Create a new archive call data2.tar.bz2 (or give it a more meaningful name if you want to version it according to year, etc) and upload.
4. Create a download link for the new archive and update in the get_tutorials.py file. (I can do this if needed. You'd just need to share the link.)

[mb2055]

Now up to date, with some new references to the RBFE snakemake workflow. Also updated reference.pdb to the new version, and updated links within all get_tutorial scripts with the new location.

[lohedges]

Thanks. We'll still need to update the README to use Python 3.11 by default along with the latest BioSImSpace. I can try testing this locally next week. (Or in a container.)

[mb2055]

I've now tested the full suite with the latest version of BSS and everything is working now that the node functionality is fixed.
The only outstanding issue is that of plumed - the conda package hasn't been updated for a long time and as such it doesn't work with any version of BSS after 2024.3. I got around this locally by building plumed from source and linking the relevant files in PATH, but this isn't really a practical long-term solution.
As a result of the plumed issue the only part of the repo that hasn't been updated is the install instructions, specifically the line mamba install -n bsstutorials -c openbiosim -c conda-forge biosimspace=2023.5.0 gromacs=2023.1 ambertools=23.3 plumed=2.9.0 cinnabar=0.3.0 pymbar=3 alchemlyb=1.0.1 as updating this to the version I used for testing would just result in an environment that doesn't resolve.

[mb2055]

Just adding a note here that following the BSS refactor, which switches to using the new sire API, there are a couple of changes that are needed to the 01_introduction tutorials:

• 01_introduction.ipynb has multiple instances of propertyKeys that need to be changed to property_keys
• 02_molecular_setup.ipynb once again has multiple instances of propertyKeys that need to be changed to property_keys