mdanalysis

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Update NCDF Reader to read .ncrst Restart Files

9

Fixes #5030 Changes made in this Pull Request: - Updated NCDF Reader to read Amber `.ncrst` restart files - Added tests to verify that the `ncrst` file is readed correctly....

jeremyleung521

feature: IMDReader Integration

12

Fixes #4827 This draft PR addresses the feature request discussed in #4827. Note: The `IMDReader` feature which was previously a part of the `imdclient` package has been moved into `MDAnalysis`...

amruthesht

Implementation of fetch_pdb()

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Fixes #4907 Changes made in this Pull Request: This is a still work in progress, but here's a implementation of @BradyAJohnston 's code wrapped into classes. I still need to...

jauy123

replaced lib.transformations with transformations package

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Fixes #5061 Changes made in this Pull Request: - removed old lib.transformations code - use transformations package instead (which is the updated version of our old vendored code) - **Makes...

orbeckst

compile failure due to numpy issues in transformations.c

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## Expected behavior ## pip install build/compiles cleanly ## Actual behavior ## See https://discord.com/channels/807348386012987462/808088023957897258/1381767573611483176 by @ljwoods2 Curious if I'm missing something, is anyone else getting a Numpy compatibility issue when...

orbeckst

the `InterRDF_s` class is significantly slower than running multiple `InterRDF` instances sequentially

1

## Expected behavior ## Recently, I have been conducting electrolyte simulation-related work using Gromacs 2025.1. Since I frequently use Python, I did not use `gmx rdf`. For multiple RDF calculations,...

gitzhangch

Feature non linear time averaged msd

1

Fixes #5028 Changes made in this Pull Request: - **msd.py** script was modified to support time-averaged mean square displacement calculation for dump files with non-linear time spacings. ## PR Checklist...

gitsirsha

issue with large dcd seeking

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Reinstalled the MDanalysis today and run rdf calculation. Got this error message "OSError: DCD seek failed with DCD error=Normal EOF" Exact same script was successfully run before with previous version...

qlearn-code

add `relprop` for atom selection and corresponding UT

2

Implementaton of #4838 Changes made in this Pull Request: - add `relprop` keyword for atom selection - add UT for this keyword I will update the User Guide once this...

ChiahsinChu

changing DL_Poly units

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Fixes #2393 Changes made in this Pull Request: - Added unit conversion to DL_Poly - ~~Removed forces from TRZ~~ - Updated test values for DL_Poly As mentioned in #2393, this...

lexi-x