orbeckst · Oct 24, 2026 · Oct 25, 2026 · IAlibay · Oct 25, 2026 · orbeckst
diff --git a/_posts/2026-10-21-release-2.11.0.md b/_posts/2026-10-21-release-2.11.0.md
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+---
+layout: post
+title: Release 2.11.0 of MDAnalysis
+---
+
+We are happy to release version 2.11.0 of MDAnalysis!
+
+This is a minor release of the MDAnalysis library; it contains bug fixes, 
+new features, and performance improvements. 
+These updates are backwards-compatible, with the exception of one API fix
+for the [AtomicDistances][] analysis, which is noted under [Changes](#changes).
+
+A highlight is the **new support for mmCIF/PDBx files**, which was one of the 
+most-requested features (see [Changes](#changes)).
+
+
+## Supported environments
+
+This release supports NumPy 2.0+ and offers backwards compatibility
+through to NumPy 1.26.0.
+
+Supported Python versions: **3.11, 3.12, 3.13, 3.14**.
+
+Supported Operating Systems:
+  - **Linux** (on [x86-64][], [ARM64][AArch64], and [ppc64le][PPC64] 
+    (conda-forge packages))
+  - **Windows** (on [x86-64][])
+  - **MacOS** (on [x86-64][] and [ARM64][])
+
+
+
+## Upgrading to MDAnalysis version 2.11.0
+
+To update with `mamba` (or `conda`) from the [conda-forge channel][] run
+
+```bash
+mamba update -c conda-forge mdanalysis
+```
+
+To update from [PyPi][] with `pip` run
+
+```bash
+python -m pip install --upgrade MDAnalysis
+```
+
+For more help with installation see the [installation instructions in the User Guide][].
+Make sure you are using a Python version compatible with MDAnalysis
+before upgrading (Python >= 3.11).
+
+
+## Notable changes
+
+For a full list of changes, enhancements, bug fixes and deprecations see the [CHANGELOG][].
+
+#### Enhancements:
+
+* Single-frame [mmCIF/PDBx][mmCIF] files, including `.cif.gz`, can now be
+  read with the optional [gemmi][] library ([Issue #2367][], [PR #4712][]):
+
+  ```python
+  import MDAnalysis as mda
+
+  u = mda.Universe("structure.cif")
+  ```
+* New `MDAnalysis.fetch.from_PDB()` helper to download structure files from
+  the RCSB Protein Data Bank (optional [pooch][] dependency). It returns a
+  path that can be passed to `Universe` ([Issue #4907][], [PR #4943][]).
+  The default download is mmCIF (`.cif.gz`); pass `file_format="pdb"` for a
+  PDB file:
+
+  ```python
+  import MDAnalysis as mda
+  from MDAnalysis.fetch import from_PDB
+
+  u = mda.Universe(from_PDB("1AKE"))
+  ```
+* New parallelization support for:
+  * `analysis.diffusionmap.DistanceMatrix` ([Issue #4679][], [PR #4745][])
+  * `analysis.atomicdistances.AtomicDistances` ([Issue #4662][], [PR #4822][])
+* DSSP analysis improvements:
+  * Proline is now included in secondary-structure assignment, following
+    the upstream PyDSSP 0.9.1 fix ([Issue #4913][], [PR #5065][])
+  * Faster distance calculations, with a selectable distance `backend`
+    (for example `"distopia"`) ([PR #5182][])
+* MOL2 files can now provide unit cell dimensions from `@<TRIPOS>CRYSIN`
+  records ([Issue #3341][], [PR #5187][])
+* GROMACS TPR reader improvements:
+  * Support for TPR files written by GROMACS 2026 ([PR #5219][])
+  * Linear angle potentials are read into the topology ([Issue #5361][], [PR #5372][])
+  * Box vectors are now read from file and available as `Universe.dimensions` 
+    ([Issue #5375][], [PR #5466][])
+* `AtomGroup.wrap()` with compounds is much faster and now scales close to
+  linearly with the number of compounds, rather than quadratically
+  ([PR #5226][])
+
+#### Fixes:
+
+* Fixed periodic-boundary handling for triclinic boxes in `apply_PBC()`
+  and in the neighbor search used by `capped_distance()` and
+  `self_capped_distance()` ([Issue #4906][], [PR #5481][]):
+  * `apply_PBC()`, `AtomGroup.wrap()` / `pack_into_box()`,
+    `center*(wrap=True)`, `AtomGroup.unwrap()` with `reference="com"` or
+    `"cog"`, and the `transformations.wrap` transformation could leave
+    atoms or compound centers outside the primary unit cell when both
+    `b_x` and `c_y` are non-zero (for example truncated octahedra). They
+    were shifted by whole box vectors, so periodic distances were
+    unaffected, but results that depend on absolute wrapped positions
+    (dipole moments, densities, written coordinates) may change.
+  * `capped_distance()` and `self_capped_distance()` with the `nsgrid` or
+    `pkdtree` methods could miss pairs within the cutoff, which also
+    affects bond guessing and distance-based selections. `nsgrid` was
+    affected in triclinic boxes with two or more non-90° angles (for
+    example a rhombic dodecahedron); `pkdtree` in boxes with both `b_x`
+    and `c_y` non-zero (for example a truncated octahedron).
+* GROMACS TPR file support fixes:
+  * Positions and velocities read from TPR files are converted to MDAnalysis
+    base units. Previously they were left in GROMACS native units
+    ([PR #5374][])
+  * Fixed reading of older TPR files written before GROMACS 5.1 (TPX version
+    < 103) ([Issue #5145][], [PR #5146][])    
+* Bond guessing now works with mixed-case atom types ([Issue #5342][], [PR #5343][])
+* NumPy boolean arrays passed to `AnalysisBase.run(frames=...)` are treated
+  as frame masks. Previously they were interpreted as integer frame indices,
+  i.e., ``True`` was parsed as frame 1 and ``False`` as frame 0, and the 
+  analysis most likely did not produce the intended output ([Issue #5472][], [PR #5476][])
+* DSSP analysis: Hydrogen-bond detection now respects periodic boundary 
+  conditions ([PR #5182][])  
+* Fixed a `TypeError` when indexing GSD trajectories with NumPy integer
+  types, which stopped analysis classes from running on those trajectories
+  ([Issue #5224][], [PR #5260][])
+* Fixed parallel reductions that produced wrong results in multiple analysis
+  classes:
+  * mean bin values in `InterRDF` ([PR #5344][])
+  * pair counts in `InterRDF_s` (wrong for one pair of groups, and an
+    error for more than two) ([Issue #5496][], [PR #5497][])
+  * eigenvectors in `GNMAnalysis` when using multiprocessing
+    ([Issue #5494][], [PR #5495][])
+
+#### Changes:
+
+* `MDAnalysis.analysis.atomicdistances.AtomicDistances` now stores its outputs
+  *inside* the `results` dictionary as `results.distances`, like other analysis
+  classes. Code that read the old attribute needs to be updated ([Issue #4819][],
+  [PR #5347][]).
+
+  This fixed an API issue in a **backwards incompatible manner**.
+* `AtomGroup.rotate()` and the `rotateby` trajectory transformation now
+  rotate velocities and forces as well as positions. The same applies to
+  `align.alignto()` and `AlignTraj`, which fit through `AtomGroup.rotate()`.
+  Previously velocities and forces were left unchanged ([Issue #5421][], [PR #5452][])
+* `WatsonCrickDist`, `MinorPairDist`, and `MajorPairDist` match the full
+  residue name. Previously only the first character was used, so names such
+  as CHARMM `DG`/`DA` or `GUA`/`ADE` were handled incorrectly. Analyses that
+  relied on the old truncation need explicit residue names via `g_name`,
+  `a_name`, and the related keyword arguments ([Issue #5360][], [PR #5365][])
+
+
+## Author statistics
+
+This release was the work of 34 contributors, **22** of which are **new contributors**.
+
+Our **new contributors** are:
+
+* @spyke7
+* @Pranay096
+* @PardhavMaradani ([GSoC contributor]({% post_url 2026-05-21-gsoc-students %}#pardhav-maradani-dashboard-for-tracking-md-simulation-progress-with-the-new-streaming-interface))
+* @tani-dubey
+* @BradyAJohnston (new [CoreDeveloper]({{ site.baseurl}}/pages/governance/#mdanalysis-core-developers))
+* @IAyaanHere
+* @khushi-phougat
+* @Dreamstick9
+* @jeremyleung521
+* @harshitgajjela-droid
+* @kunjsinha ([GSoC contributor]({% post_url 2026-05-21-gsoc-students %}#kunj-sinha-interface-for-post-simulation-analysis-crawling-of-westpa-simulations-))
+* @aygarwal
+* @ParthUppal523
+* @ollyfutur
+* @Amarendra22
+* @shubhammittal2241
+* @charity-g
+* @saiudayagiri
+* @apoorva-01
+* @Aryaman-Chaudhri
+* @sici17
+* @AkshitBoora
+
+
+## Acknowledgements
+
+MDAnalysis thanks [NumFOCUS][] for its continued support as our fiscal sponsor,
+the [Chan Zuckerberg Initiative][] for supporting MDAnalysis under an EOSS5 award,
+and the [National Science Foundation][NSF] for support under CSSI award
+[2311372][NSF CSSI 2311372].
+
+— @IAlibay on behalf of the [MDAnalysis Team][]
+
+
+----
+
+[AtomicDistances]: https://docs.mdanalysis.org/2.11.0/documentation_pages/analysis/atomicdistances.html#MDAnalysis.analysis.atomicdistances.AtomicDistances
+[x86-64]: https://en.wikipedia.org/wiki/X86-64
+[AArch64]: https://en.wikipedia.org/wiki/AArch64
+[ARM64]: https://en.wikipedia.org/wiki/Apple_M1
+[PPC64]: https://en.wikipedia.org/wiki/Ppc64
+[installation instructions in the User Guide]: https://userguide.mdanalysis.org/stable/installation.html
+[conda-forge channel]: https://anaconda.org/conda-forge/mdanalysis
+[PyPi]: https://pypi.org/project/MDAnalysis/
+[NumFOCUS]: https://www.numfocus.org
+[CHANGELOG]: https://github.com/MDAnalysis/mdanalysis/blob/release-2.11.0/package/CHANGELOG
+[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/
+[NSF]: https://www.nsf.gov
+[NSF CSSI 2311372]: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2311372
+[MDAnalysis Team]: {{ site.baseurl }}/pages/team
+[mmCIF]: https://mmcif.wwpdb.org/
+[gemmi]: https://gemmi.readthedocs.io/
+[pooch]: https://www.fatiando.org/pooch/latest/
+[Issue #4679]: https://github.com/MDAnalysis/mdanalysis/issues/4679
+[PR #4745]: https://github.com/MDAnalysis/mdanalysis/pull/4745
+[Issue #4662]: https://github.com/MDAnalysis/mdanalysis/issues/4662
+[PR #4822]: https://github.com/MDAnalysis/mdanalysis/pull/4822
+[Issue #4913]: https://github.com/MDAnalysis/mdanalysis/issues/4913
+[PR #5065]: https://github.com/MDAnalysis/mdanalysis/pull/5065
+[PR #5182]: https://github.com/MDAnalysis/mdanalysis/pull/5182
+[Issue #2367]: https://github.com/MDAnalysis/mdanalysis/issues/2367
+[PR #4712]: https://github.com/MDAnalysis/mdanalysis/pull/4712
+[Issue #4907]: https://github.com/MDAnalysis/mdanalysis/issues/4907
+[PR #4943]: https://github.com/MDAnalysis/mdanalysis/pull/4943
+[Issue #3341]: https://github.com/MDAnalysis/mdanalysis/issues/3341
+[PR #5187]: https://github.com/MDAnalysis/mdanalysis/pull/5187
+[PR #5219]: https://github.com/MDAnalysis/mdanalysis/pull/5219
+[Issue #5361]: https://github.com/MDAnalysis/mdanalysis/issues/5361
+[PR #5372]: https://github.com/MDAnalysis/mdanalysis/pull/5372
+[Issue #5375]: https://github.com/MDAnalysis/mdanalysis/issues/5375
+[PR #5466]: https://github.com/MDAnalysis/mdanalysis/pull/5466
+[PR #5226]: https://github.com/MDAnalysis/mdanalysis/pull/5226
+[PR #5374]: https://github.com/MDAnalysis/mdanalysis/pull/5374
+[Issue #5145]: https://github.com/MDAnalysis/mdanalysis/issues/5145
+[PR #5146]: https://github.com/MDAnalysis/mdanalysis/pull/5146
+[Issue #4906]: https://github.com/MDAnalysis/mdanalysis/issues/4906
+[PR #5481]: https://github.com/MDAnalysis/mdanalysis/pull/5481
+[Issue #5472]: https://github.com/MDAnalysis/mdanalysis/issues/5472
+[PR #5476]: https://github.com/MDAnalysis/mdanalysis/pull/5476
+[Issue #5224]: https://github.com/MDAnalysis/mdanalysis/issues/5224
+[PR #5260]: https://github.com/MDAnalysis/mdanalysis/pull/5260
+[PR #5344]: https://github.com/MDAnalysis/mdanalysis/pull/5344
+[Issue #5496]: https://github.com/MDAnalysis/mdanalysis/issues/5496
+[PR #5497]: https://github.com/MDAnalysis/mdanalysis/pull/5497
+[Issue #5494]: https://github.com/MDAnalysis/mdanalysis/issues/5494
+[PR #5495]: https://github.com/MDAnalysis/mdanalysis/pull/5495
+[Issue #5342]: https://github.com/MDAnalysis/mdanalysis/issues/5342
+[PR #5343]: https://github.com/MDAnalysis/mdanalysis/pull/5343
+[Issue #4819]: https://github.com/MDAnalysis/mdanalysis/issues/4819
+[PR #5347]: https://github.com/MDAnalysis/mdanalysis/pull/5347
+[Issue #5421]: https://github.com/MDAnalysis/mdanalysis/issues/5421
+[PR #5452]: https://github.com/MDAnalysis/mdanalysis/pull/5452
+[Issue #5360]: https://github.com/MDAnalysis/mdanalysis/issues/5360
+[PR #5365]: https://github.com/MDAnalysis/mdanalysis/pull/5365