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IAlibay merged 3 commits into from
Mar 10, 2025
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ENH: tpx 137 (GROMACS 2025.0) support #4919

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66d9277
ENH: tpx 137 support
tylerjereddy Feb 15, 2025
2522224
TST: Add GROMACS 2025.0 TPR with NNpot
al42and Mar 2, 2025
cd912fd
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IAlibay Mar 10, 2025
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4 changes: 2 additions & 2 deletions package/CHANGELOG
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions package/MDAnalysis/topology/TPRParser.py
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Expand Up @@ -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.
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6 changes: 4 additions & 2 deletions package/MDAnalysis/topology/tpr/setting.py
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Expand Up @@ -53,6 +53,7 @@
129,
133,
134,
137,
)

# Some constants
Expand Down Expand Up @@ -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``
Expand Down Expand Up @@ -127,6 +128,7 @@
(tpxv_GenericInternalParameters, F_DENSITYFITTING),
(tpxv_VSite1, F_VSITE1),
(tpxv_VSite2FD, F_VSITE2FD),
(137, F_ENNPOT),
]
# fmt: on

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4 changes: 4 additions & 0 deletions package/MDAnalysis/topology/tpr/utils.py
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Expand Up @@ -702,6 +702,10 @@
elif i in [setting.F_CMAP]:
data.unpack_int() # cmap.cmapA
data.unpack_int() # cmap.cmapB
elif i in [setting.F_ENNPOT]:

Check warning on line 705 in package/MDAnalysis/topology/tpr/utils.py

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# TODO: handle the new neural network potentials
# supported from GROMACS 2025.0
pass

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@tylerjereddy tylerjereddy Feb 18, 2025

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For this and other new v2025.0 bells and whistles, cc @al42and for possible generation of new test files that have the new bells and whistles.

I don't now if we really need a new test file with i.e., the new PyTorch potential handling + reference coordinate scaling with multiple centers of mass + init-histogram-counts to enable continuation of expanded ensemble runs.

Probably would be good to have eventually, if only to make sure we don't need to skip over any other bits of information when "seeking" through the file.

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@IAlibay IAlibay Feb 20, 2025

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Do we think there are attributes we will be missing if we're not properly parsing the NN potential things? i.e. what I'm asking is if we need a warning here.

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@al42and al42and Feb 22, 2025

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For this and other new v2025.0 bells and whistles, cc @al42and for possible generation of new test files that have the new bells and whistles.

I can make a TPR with a bunch of things turned on, but there are issues if we want to stick with existing test sets:

  • 2lyz: they only have TPR, which is neither editable nor "decompilable" into parts; can't change settings there (and looks like the original receipt is lost in time, since the new are just converted from the old ones, per 336ff1d).
  • bonded/dummy: currently, for NN, we need something with "physical" element names.

If that's ok, I can create a new TPR roughly based on GROMACS's own tests.
Reconstructing 2lyz and making a test based on it is doable, but I'd rather avoid that as long as you're ok with adding a new test system.

else:
raise NotImplementedError(f"unknown functype: {i}")
return
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Binary file added testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2025_0.tpr
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Binary file added testsuite/MDAnalysisTests/data/tprs/ala_nnpot_gmx_2025_0.tpr
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Binary file added testsuite/MDAnalysisTests/data/tprs/all_bonded/dummy_2025_0.tpr
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Binary file added testsuite/MDAnalysisTests/data/tprs/virtual_sites/extra-interactions-2025_0.tpr
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13 changes: 13 additions & 0 deletions testsuite/MDAnalysisTests/datafiles.py
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Expand Up @@ -133,6 +133,7 @@
"TPR2023",
"TPR2024",
"TPR2024_4",
"TPR2025_0",
"TPR510_bonded",
"TPR2016_bonded",
"TPR2018_bonded",
Expand All @@ -147,6 +148,7 @@
"TPR2023_bonded",
"TPR2024_bonded",
"TPR2024_4_bonded",
"TPR2025_0_bonded",
"TPR_EXTRA_2021",
"TPR_EXTRA_2020",
"TPR_EXTRA_2018",
Expand All @@ -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",
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -612,6 +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()
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Outdated

XYZ_psf = (_data_ref / "2r9r-1b.psf").as_posix()
XYZ_bz2 = (_data_ref / "2r9r-1b.xyz.bz2").as_posix()
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34 changes: 31 additions & 3 deletions testsuite/MDAnalysisTests/topology/test_tprparser.py
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Expand Up @@ -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,
Expand All @@ -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
Expand All @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -205,6 +211,18 @@ class TestTPR46x(TPRAttrs):
def filename(self, request):
return request.param

class TestTPRNnpot(TPRAttrs):
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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):
"""
Expand Down Expand Up @@ -315,7 +333,7 @@ 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
Expand All @@ -338,6 +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",
(
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