Irfan Alibay

FIREMinimizationIntegrator fails on explicitly solvated system using CPU platform

3

## Context This is related to why #684 needed fixing, and hopefully some of the alchemical pains here will go away with #672 ## Bug report We noticed that the...

[HybridTopologyFactory] Copying virtual sites from old/new systems to hybrid system leads to exception

2

## Expected behaviour Passing a system with virtual sites in the non-core, non-unique portions of the old & new systems, should lead to those virtual sites existing in the hybrid...

Make passing user supplied partial charges to SystemGenerator an explicit keyword?

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Currently SystemGenerator does the following: - If there are partial charges present on the OFF molecule use them directly (i.e. don't generate new charges) - Unless these partial charges are...

Allow passing a toolkit registry through to SystemGenerator

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The template generators do: 1. A lot of `to_smiles` and `from_smiles` calls when caching parameters. 2. A toolkit dependent openmm system creation call. It would be great if we could...

Follow up from https://github.com/MDAnalysis/mdanalysis/pull/4580 Once mypy works with a more modern version of rdkit, unpin the version on the action.

Merge 3.0 pending PRs

7

Here is a list of PRs that need merging for the 3.0 release (but not before): - [ ] https://github.com/MDAnalysis/mdanalysis/pull/4532#issuecomment-2021634120 _note: please edit directly and add to this list as...

Mostly a test for if this will work with the current macos runner Adds: - [ ] workflow trigger - [ ] cron trigger

Document expected standard residues

6

Apologies if I'm missing something obvious here. My understanding is that propka expects certain standard residues (defined [here](https://github.com/jensengroup/propka/blob/831e7380689b05892645012766671e2df8a644d8/propka/lib.py#L20-L23)) as `ATOM` entries in the input PDB and that other "non-standard" residues...

License incompatible with target core library license?

6

I think? LGPLv3 means that we can't keep this as a core dependency of MDAnalysis and also aim for LGPLv2.1.

Auto-populate authors in docs

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Authors are currently hard coded in the docs build. We probably would want to auto-populate it in the same way we do for other MDA projects?