Add GROMACS 2025.0 TPR with NNpot

Generated input file with random set of features enabled
Using inputs from gromacs/src/testutils/simulationdatabase/
`gmx grompp -f tt6710474.mdp -c  ala.gro -n ala.ndx -p ala.top  -o ala_nnpot_gmx_2025_0.tpr`

Author: al42and

testsuite/MDAnalysisTests/data/tprs/ala_nnpot_gmx_2025_0.tpr

@@ -159,6 +159,7 @@
     "TPR_EXTRA_2024",
     "TPR_EXTRA_2024_4",
     "TPR_EXTRA_2025_0",
+    "TPR_NNPOT_2025_0",
     "PDB_sub_sol",
     "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
@@ -620,6 +621,10 @@
 TPR_EXTRA_407 = (
     _data_ref / "tprs/virtual_sites/extra-interactions-4.0.7.tpr"
 ).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()
 
 XYZ_psf = (_data_ref / "2r9r-1b.psf").as_posix()
 XYZ_bz2 = (_data_ref / "2r9r-1b.xyz.bz2").as_posix()

testsuite/MDAnalysisTests/datafiles.py

@@ -49,8 +49,8 @@
                                         TPR2021_bonded, TPR2021_double_bonded,
                                         TPR2021Double, TPR2022RC1_bonded,
                                         TPR2023_bonded, TPR2024_4_bonded,
-                                        TPR2025_0_bonded,
-                                        TPR2024_bonded)
+                                        TPR2025_0_bonded, TPR2024_bonded,
+                                        TPR_NNPOT_2025_0)
 from numpy.testing import assert_equal
 
 # fmt: on
@@ -211,6 +211,18 @@ class TestTPR46x(TPRAttrs):
     def filename(self, request):
         return request.param
 
+class TestTPRNnpot(TPRAttrs):
+    expected_n_atoms = 23
+    expected_n_residues = 2
+    expected_n_segments = 1
+    ref_moltypes = np.array(["Protein_chain_A"] * 2, dtype=object)
+    ref_molnums = np.array([0] * 2)
+    ref_chainIDs = ["A"]
+
+    @pytest.fixture(params=[TPR_NNPOT_2025_0])
+    def filename(self, request):
+        return request.param
+
 
 def _test_is_in_topology(name, elements, topology_path, topology_section):
     """
@@ -344,6 +356,16 @@ def test_settle(bonds_water):
     assert bonds_water[-1][1] == 2262
 
 
+@pytest.mark.parametrize("tpr_path", [TPR_NNPOT_2025_0])
+def test_ala2(tpr_path):
+    topology = MDAnalysis.topology.TPRParser.TPRParser(tpr_path).parse()
+    # Check that bonds etc are read correctly
+    assert len(topology.bonds.values) == 22  # 12 Bond + 10 Connect
+    assert len(topology.angles.values) == 21  # 21 Angle
+    assert len(topology.dihedrals.values) == 26  # 26 Proper Dih.
+    assert len(topology.impropers.values) == 1  # 1 Per. Imp. Dih.
+
+
 @pytest.mark.parametrize(
     "tpr_path, expected_exception",
     (