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I would like to open some discussion about using `MDAnalysis` glue. This would require conversions from `gmso.core.Topology` to some `MDAnalysis` object - probably `Universe`? It is an appealing idea …
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I moved the MDAnalysis SPIDAL tutorial from Becksteinlab to the MDAnalysis org in d19258c . I changed all the paths in the notebook and in the PPTX.
@iparask – I don't remember if the PPT in this r…
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https://userguide.mdanalysis.org/stable/formats/reference/tpr.html#supported-versions
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## Is your feature request related to a problem? ##
The LeafletFinder function will be removed in MDAnalysis 3.0.0 (see https://github.com/MDAnalysis/mdanalysis/issues/4544#issue-2216069497)
## De…
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The `nanover-omni` package is missing from the modules:
![image](https://github.com/user-attachments/assets/4d5d3c50-1b77-4877-b18d-ee0c1512aeca)
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Files from https://acs.figshare.com/articles/dataset/Small_Molecule_Solvation_Free_Energy_Enhanced_Conformational_Sampling_Using_Expanded_Ensemble_Molecular_Dynamics_Simulation/2615170 have some issue…
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The first step of this OpenBabel converter will be to convert OpenBabel OBMols to MDAnalysis AtomGroups. This will enable the indirect parsing of over 100 file types into a format that MDAnalysis tool…
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During the [Governance and Docs Meeting](https://docs.google.com/document/d/1TmV9ZDu21C2BJwdBxN1jkkdhMUsrOYIn_J_nMZjKyfM/edit?usp=sharing) on July 29th, it was pointed out that we suggest reaching out…
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I see this error when processing pdb files with residue numbers into the thousands, which shifts over column placement starting at the residue number:
Input:
```
ATOM 16105 N GLN D 998 4…
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We are getting a lot of "duplicate label" issues when building the docs.
Took me far too long to debug, but it turns out that the issue is that we have parts of the docs that appear twice under two…