ENH: tpx 138 (GROMACS 2026.0) support (#5219)

* ENH: tpx 138 (GROMACS 2026.0) support (TPX generation 29)
* Add .tpr parsing support for GROMACS 2026.0, which was recently released: https://manual.gromacs.org/2026.0/release-notes/2026/major/highlights.html
* test file generation:  used gmx convert-tpr with GROMACS 2026.0 on the alanine dipeptide NN potential .tpr provided back in gh-4919. 

---------

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Author: tylerjereddy

package/CHANGELOG

@@ -37,6 +37,7 @@ Fixes
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
 
 Enhancements
+ * Adds support for parsing `.tpr` files produced by GROMACS 2026.0
  * Enables parallelization for analysis.diffusionmap.DistanceMatrix
    (Issue #4679, PR #4745)
 

package/MDAnalysis/topology/TPRParser.py

@@ -69,6 +69,7 @@
    133        28             2024.1               yes
    134        28             2024.4               yes
    137        28             2025.0               yes
+   138        29             2026.0               yes
    ========== ============== ==================== =====
 
 .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.

package/MDAnalysis/topology/tpr/setting.py

@@ -54,6 +54,7 @@
     133,
     134,
     137,
+    138,
 )
 
 # Some constants

testsuite/MDAnalysisTests/coordinates/test_tpr.py

@@ -64,6 +64,7 @@
     TPR455Double,
     TPR_xvf_2024_4,
     TPR_NNPOT_2025_0,
+    TPR_NNPOT_2026_0,
     TPR2020B2,
     INPCRD,
     TPR_gh_5145,
@@ -82,6 +83,14 @@
         # this case is an alanine dipeptide
         # with neural network potential active
         # and nonzero velocities
+        (
+            TPR_NNPOT_2026_0,  # tpx 138
+            [2.36700e00, 2.30000e-02, 9.20000e-02],
+            [2.95100e00, 2.00000e-01, 2.41000e-01],
+            (23, 3),
+            [-4.72100e-01, -2.20900e-01, -2.42800e-01],
+            [-1.11900e-01, -3.69300e-01, -6.10000e-03],
+        ),
         (
             TPR_NNPOT_2025_0,  # tpx 137
             [2.36700e00, 2.30000e-02, 9.20000e-02],

testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2026_0.tpr

@@ -136,6 +136,7 @@
     "TPR2024",
     "TPR2024_4",
     "TPR2025_0",
+    "TPR2026_0",
     "TPR510_bonded",
     "TPR2016_bonded",
     "TPR2018_bonded",
@@ -151,6 +152,7 @@
     "TPR2024_bonded",
     "TPR2024_4_bonded",
     "TPR2025_0_bonded",
+    "TPR2026_0_bonded",
     "TPR_EXTRA_2021",
     "TPR_EXTRA_2020",
     "TPR_EXTRA_2018",
@@ -161,7 +163,9 @@
     "TPR_EXTRA_2024",
     "TPR_EXTRA_2024_4",
     "TPR_EXTRA_2025_0",
+    "TPR_EXTRA_2026_0",
     "TPR_NNPOT_2025_0",
+    "TPR_NNPOT_2026_0",
     "PDB_sub_sol",
     "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
@@ -568,6 +572,7 @@
 TPR2024 = (_data_ref / "tprs/2lyz_gmx_2024.tpr").as_posix()
 TPR2024_4 = (_data_ref / "tprs/2lyz_gmx_2024_4.tpr").as_posix()
 TPR2025_0 = (_data_ref / "tprs/2lyz_gmx_2025_0.tpr").as_posix()
+TPR2026_0 = (_data_ref / "tprs/2lyz_gmx_2026_0.tpr").as_posix()
 # double precision
 TPR455Double = (_data_ref / "tprs/drew_gmx_4.5.5.double.tpr").as_posix()
 TPR460 = (_data_ref / "tprs/ab42_gmx_4.6.tpr").as_posix()
@@ -600,7 +605,11 @@
 TPR2024_bonded = (_data_ref / "tprs/all_bonded/dummy_2024.tpr").as_posix()
 TPR2024_4_bonded = (_data_ref / "tprs/all_bonded/dummy_2024_4.tpr").as_posix()
 TPR2025_0_bonded = (_data_ref / "tprs/all_bonded/dummy_2025_0.tpr").as_posix()
+TPR2026_0_bonded = (_data_ref / "tprs/all_bonded/dummy_2026_0.tpr").as_posix()
 # all interactions
+TPR_EXTRA_2026_0 = (
+    _data_ref / "tprs/virtual_sites/extra-interactions-2026_0.tpr"
+).as_posix()
 TPR_EXTRA_2025_0 = (
     _data_ref / "tprs/virtual_sites/extra-interactions-2025_0.tpr"
 ).as_posix()
@@ -633,6 +642,7 @@
 ).as_posix()
 # ALA dipeptide with neural network potential and a few other options
 TPR_NNPOT_2025_0 = (_data_ref / "tprs/ala_nnpot_gmx_2025_0.tpr").as_posix()
+TPR_NNPOT_2026_0 = (_data_ref / "tprs/ala_nnpot_gmx_2026_0.tpr").as_posix()
 
 XYZ_psf = (_data_ref / "2r9r-1b.psf").as_posix()
 XYZ_bz2 = (_data_ref / "2r9r-1b.xyz.bz2").as_posix()

testsuite/MDAnalysisTests/data/tprs/ala_nnpot_gmx_2026_0.tpr

@@ -34,13 +34,13 @@
                                         TPR2016, TPR2018, TPR2019B3, TPR2020,
                                         TPR2020B2, TPR2021, TPR2022RC1,
                                         TPR2023, TPR2024, TPR2024_4,
-                                        TPR2025_0,
+                                        TPR2025_0, TPR2026_0,
                                         TPR_EXTRA_407, TPR_EXTRA_2016,
                                         TPR_EXTRA_2018, TPR_EXTRA_2020,
                                         TPR_EXTRA_2021, TPR_EXTRA_2022RC1,
                                         TPR_EXTRA_2023, TPR_EXTRA_2024,
                                         TPR_EXTRA_2024_4, XTC, TPR334_bonded,
-                                        TPR_EXTRA_2025_0,
+                                        TPR_EXTRA_2025_0, TPR_EXTRA_2026_0,
                                         TPR455Double, TPR510_bonded,
                                         TPR2016_bonded, TPR2018_bonded,
                                         TPR2019B3_bonded, TPR2020_bonded,
@@ -50,7 +50,8 @@
                                         TPR2021Double, TPR2022RC1_bonded,
                                         TPR2023_bonded, TPR2024_4_bonded,
                                         TPR2025_0_bonded, TPR2024_bonded,
-                                        TPR_NNPOT_2025_0)
+                                        TPR2026_0_bonded,
+                                        TPR_NNPOT_2025_0, TPR_NNPOT_2026_0)
 from numpy.testing import assert_equal
 
 # fmt: on
@@ -70,6 +71,8 @@
     TPR2024_bonded,
     TPR2024_4_bonded,
     TPR2025_0_bonded,
+    TPR2026_0_bonded,
+    TPR_EXTRA_2026_0,
     TPR_EXTRA_2025_0,
     TPR_EXTRA_2024_4,
     TPR_EXTRA_2024,
@@ -154,7 +157,7 @@ class TestTPRGromacsVersions(TPRAttrs):
             TPR451, TPR452, TPR453, TPR454, TPR455, TPR502, TPR504, TPR505,
             TPR510, TPR2016, TPR2018, TPR2019B3, TPR2020, TPR2020Double,
             TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024, TPR2024_4,
-            TPR2025_0,
+            TPR2025_0, TPR2026_0,
         ]
     )
     # fmt: on
@@ -220,7 +223,7 @@ class TestTPRNnpot(TPRAttrs):
     ref_molnums = np.array([0] * 2)
     ref_chainIDs = ["A"]
 
-    @pytest.fixture(params=[TPR_NNPOT_2025_0])
+    @pytest.fixture(params=[TPR_NNPOT_2025_0, TPR_NNPOT_2026_0])
     def filename(self, request):
         return request.param
 
@@ -357,7 +360,7 @@ def test_settle(bonds_water):
     assert bonds_water[-1][1] == 2262
 
 
-@pytest.mark.parametrize("tpr_path", [TPR_NNPOT_2025_0])
+@pytest.mark.parametrize("tpr_path", [TPR_NNPOT_2025_0, TPR_NNPOT_2026_0])
 def test_ala2(tpr_path):
     topology = MDAnalysis.topology.TPRParser.TPRParser(tpr_path).parse()
     # Check that bonds etc are read correctly