ENH: tpx 137 (GROMACS 2025.0) support (#4919)

* ENH: tpx 137 support

* Add support for GROMACS `2025.0` `.tpr` version 137, which mostly
involves accounting for the new PyTorch neural network potential
field, `F_ENNPOT`. Most of the other changes are similar to the
approach I previously used for bumping `.tpr` version support
in gh-4866.

* Some other `.tpr` additions are noted at #4888,
but we don't appear to need to use those within the context of our
current `.tpr` parsing tests. It may be sensible to occasionally
generate `.tpr` test files that use those extra bells and whistles to
see how we fare, though as a first pass here the full testsuite passes
for us if we simply do the usual `gmx convert-tpr` at the latest stable
GROMACS release tag `v2025.0` and propagate our current TPR testing
to additionally use the converted files.

* TST: 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`

* Add Andrey to `CHANGELOG`

* Apply suggestions from code review

---------

Co-authored-by: Andrey Alekseenko <al42and@gmail.com>

Author: tylerjereddy

package/CHANGELOG

@@ -15,12 +15,12 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
-         marinegor, hmacdope, jauy123
+         marinegor, hmacdope, jauy123, al42and
 
  * 2.9.0
 
 Fixes
- * Add support for TPR files produced by GROMACS 2024.4
+ * Add support for TPR files produced by GROMACS 2024.4 and GROMACS 2025.0
  * Fixes invalid default unit from Angstrom to Angstrom^{-3} for convert_density() function. (Issue #4829)
  * Fixes deprecation warning Array to scalar convertion. Replaced atan2() with np.arctan2() (Issue #4339)
  * Replaced mutable defaults with None and initialized them within

package/MDAnalysis/topology/TPRParser.py

@@ -68,6 +68,7 @@
    129        28             2023                 yes
    133        28             2024.1               yes
    134        28             2024.4               yes
+   137        28             2025.0               yes
    ========== ============== ==================== =====
 
 .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.

package/MDAnalysis/topology/tpr/setting.py

@@ -53,6 +53,7 @@
     129,
     133,
     134,
+    137,
 )
 
 # Some constants
@@ -94,12 +95,12 @@
     F_DIHRESVIOL, F_CONSTR, F_CONSTRNC, F_SETTLE, F_VSITE1,
     F_VSITE2, F_VSITE2FD, F_VSITE3, F_VSITE3FD, F_VSITE3FAD,
     F_VSITE3OUT, F_VSITE4FD, F_VSITE4FDN, F_VSITEN,
-    F_COM_PULL, F_DENSITYFITTING, F_EQM, F_EPOT, F_EKIN,
+    F_COM_PULL, F_DENSITYFITTING, F_EQM, F_ENNPOT, F_EPOT, F_EKIN,
     F_ETOT, F_ECONSERVED, F_TEMP, F_VTEMP_NOLONGERUSED,
     F_PDISPCORR, F_PRES, F_DHDL_CON, F_DVDL,
     F_DKDL, F_DVDL_COUL, F_DVDL_VDW, F_DVDL_BONDED,
     F_DVDL_RESTRAINT, F_DVDL_TEMPERATURE, F_NRE
-) = list(range(95))
+) = list(range(96))
 # fmt: on
 
 #: Function types from ``<gromacs_dir>/src/gmxlib/tpxio.c``
@@ -127,6 +128,7 @@
     (tpxv_GenericInternalParameters, F_DENSITYFITTING),
     (tpxv_VSite1, F_VSITE1),
     (tpxv_VSite2FD, F_VSITE2FD),
+    (137, F_ENNPOT),
 ]
 # fmt: on
 

package/MDAnalysis/topology/tpr/utils.py

@@ -702,6 +702,10 @@ def do_iparams(data, functypes, fver):
         elif i in [setting.F_CMAP]:
             data.unpack_int()  # cmap.cmapA
             data.unpack_int()  # cmap.cmapB
+        elif i in [setting.F_ENNPOT]:
+            # TODO: handle the new neural network potentials
+            # supported from GROMACS 2025.0
+            pass
         else:
             raise NotImplementedError(f"unknown functype: {i}")
     return

testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2025_0.tpr

@@ -133,6 +133,7 @@
     "TPR2023",
     "TPR2024",
     "TPR2024_4",
+    "TPR2025_0",
     "TPR510_bonded",
     "TPR2016_bonded",
     "TPR2018_bonded",
@@ -147,6 +148,7 @@
     "TPR2023_bonded",
     "TPR2024_bonded",
     "TPR2024_4_bonded",
+    "TPR2025_0_bonded",
     "TPR_EXTRA_2021",
     "TPR_EXTRA_2020",
     "TPR_EXTRA_2018",
@@ -156,6 +158,8 @@
     "TPR_EXTRA_2023",
     "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",
@@ -553,6 +557,7 @@
 TPR2023 = (_data_ref / "tprs/2lyz_gmx_2023.tpr").as_posix()
 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()
 # 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()
@@ -584,7 +589,11 @@
 TPR2023_bonded = (_data_ref / "tprs/all_bonded/dummy_2023.tpr").as_posix()
 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()
 # all interactions
+TPR_EXTRA_2025_0 = (
+    _data_ref / "tprs/virtual_sites/extra-interactions-2025_0.tpr"
+).as_posix()
 TPR_EXTRA_2024_4 = (
     _data_ref / "tprs/virtual_sites/extra-interactions-2024_4.tpr"
 ).as_posix()
@@ -612,6 +621,8 @@
 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/data/tprs/ala_nnpot_gmx_2025_0.tpr

@@ -34,11 +34,13 @@
                                         TPR2016, TPR2018, TPR2019B3, TPR2020,
                                         TPR2020B2, TPR2021, TPR2022RC1,
                                         TPR2023, TPR2024, TPR2024_4,
+                                        TPR2025_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,
                                         TPR455Double, TPR510_bonded,
                                         TPR2016_bonded, TPR2018_bonded,
                                         TPR2019B3_bonded, TPR2020_bonded,
@@ -47,7 +49,8 @@
                                         TPR2021_bonded, TPR2021_double_bonded,
                                         TPR2021Double, TPR2022RC1_bonded,
                                         TPR2023_bonded, TPR2024_4_bonded,
-                                        TPR2024_bonded)
+                                        TPR2025_0_bonded, TPR2024_bonded,
+                                        TPR_NNPOT_2025_0)
 from numpy.testing import assert_equal
 
 # fmt: on
@@ -66,6 +69,8 @@
     TPR2023_bonded,
     TPR2024_bonded,
     TPR2024_4_bonded,
+    TPR2025_0_bonded,
+    TPR_EXTRA_2025_0,
     TPR_EXTRA_2024_4,
     TPR_EXTRA_2024,
     TPR_EXTRA_2023,
@@ -148,7 +153,8 @@ class TestTPRGromacsVersions(TPRAttrs):
             TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, TPR450,
             TPR451, TPR452, TPR453, TPR454, TPR455, TPR502, TPR504, TPR505,
             TPR510, TPR2016, TPR2018, TPR2019B3, TPR2020, TPR2020Double,
-            TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024, TPR2024_4
+            TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024, TPR2024_4,
+            TPR2025_0,
         ]
     )
     # fmt: on
@@ -206,6 +212,19 @@ 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):
     """
     Test if an interaction appears as expected in the topology
@@ -315,7 +334,7 @@ def test_all_impropers(topology, impr):
 @pytest.fixture(params=(
         TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, TPR450,
         TPR451, TPR452, TPR453, TPR454, TPR502, TPR504, TPR505, TPR510,
-        TPR2016, TPR2018, TPR2023, TPR2024, TPR2024_4,
+        TPR2016, TPR2018, TPR2023, TPR2024, TPR2024_4, TPR2025_0,
     )
 )
 # fmt: on
@@ -338,6 +357,16 @@ 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",
     (