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ENH: support GMX linear angle potential #5372

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ENH: support GMX linear angle potential
tylerjereddy May 2, 2026
8960349
Merge branch 'develop' into treddy_issue_5361
orbeckst May 30, 2026
42c7425
Update CHANGELOG
orbeckst May 30, 2026
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,8 @@ Fixes
DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)

Enhancements
* Read Linear Angle bonded interaction entries from GROMACS TPR files and
add the angles to the topology (Issue #5361, PR #5372)
Comment on lines +63 to +64
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@orbeckst orbeckst May 30, 2026

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@tylerjereddy please check that you're happy with the entry

* Enables parallelization for analysis.atomicdistances.AtomicDistances
(Issue #4662, PR #4822)
* DSSP uses ``capped_distance`` and ``calc_bonds`` for faster distance
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2 changes: 1 addition & 1 deletion package/MDAnalysis/topology/tpr/utils.py
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Expand Up @@ -826,7 +826,7 @@ def do_moltype(data, symtab, fver):
bonds += list(ik_obj.process(ias))
elif ik_obj.name in ['ANGLES', 'G96ANGLES', 'CROSS_BOND_BOND',
'CROSS_BOND_ANGLE', 'UREY_BRADLEY', 'QANGLES',
'RESTRANGLES', 'TABANGLES']:
'RESTRANGLES', 'TABANGLES', 'LINEAR_ANGLES']:
angles += list(ik_obj.process(ias))
elif ik_obj.name in ['PDIHS', 'RBDIHS', 'RESTRDIHS', 'CBTDIHS',
'FOURDIHS', 'TABDIHS']:
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11 changes: 11 additions & 0 deletions testsuite/MDAnalysisTests/coordinates/test_tpr.py
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Expand Up @@ -68,6 +68,7 @@
TPR2020B2,
INPCRD,
TPR_gh_5145,
TPR_linear_angle,
)
import MDAnalysis as mda
from MDAnalysis.coordinates.TPR import TPRReader
Expand All @@ -84,6 +85,16 @@
# NOTE: expected values are expressed in nm
# units and converted to Angstrom in the body
# of the test below, before assertions

# see gh-5361 for CO2/linear angle:
(
TPR_linear_angle,
[1.250, 1.250, 1.250],
[1.250, 1.260, 1.136],
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@tylerjereddy tylerjereddy May 3, 2026

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I think we may have a problem here with the TPR coordinate parsing using nm instead of MDA A units. The correponding .gro file has nm units which match our parse here, but I don't think we want to match nm?

CO2 hydrate + Mix(CO2 + H2O)
    3
    1CO2      C    1   1.250   1.250   1.250
    1CO2     O1    2   1.250   1.239   1.365
    1CO2     O2    3   1.250   1.260   1.136
   2.50000   2.50000   2.50000

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@tylerjereddy tylerjereddy May 3, 2026

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That's a separate matter if I'm right though..

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@orbeckst orbeckst May 30, 2026

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For completeness: #5373 was addressed by you :-)

(3, 3),
[0, 0, 0],
[0, 0, 0],
),
# this case is an alanine dipeptide
# with neural network potential active
# and nonzero velocities
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Binary file added testsuite/MDAnalysisTests/data/tprs/Linear_Angle.tpr
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2 changes: 2 additions & 0 deletions testsuite/MDAnalysisTests/datafiles.py
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Expand Up @@ -137,6 +137,7 @@
"TPR2024_4",
"TPR2025_0",
"TPR2026_0",
"TPR_linear_angle",
"TPR510_bonded",
"TPR2016_bonded",
"TPR2018_bonded",
Expand Down Expand Up @@ -574,6 +575,7 @@
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()
TPR_linear_angle = (_data_ref / "tprs/Linear_Angle.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()
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12 changes: 11 additions & 1 deletion testsuite/MDAnalysisTests/topology/test_tprparser.py
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Expand Up @@ -51,7 +51,8 @@
TPR2023_bonded, TPR2024_4_bonded,
TPR2025_0_bonded, TPR2024_bonded,
TPR2026_0_bonded,
TPR_NNPOT_2025_0, TPR_NNPOT_2026_0)
TPR_NNPOT_2025_0, TPR_NNPOT_2026_0,
TPR_linear_angle)
from numpy.testing import assert_equal

# fmt: on
Expand Down Expand Up @@ -438,3 +439,12 @@ def test_resids(resid_from_one, resid_addition):
resids,
err_msg="tpr_resid_from_one kwarg not switching resids",
)


def test_gh_5361():
# GROMACS linear angle potential handling with CO2 example
u = mda.Universe(TPR_linear_angle)
actual = u.angles.to_indices()
expected = [[1, 0, 2]]
assert_equal(u.atoms.names, ["C", "O1", "O2"])
assert_equal(actual, expected)
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