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Fix #232 #233

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merged 4 commits into from
Oct 9, 2024
Merged

Fix #232 #233

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17915cf
Proper length of the custom_clj_params used for positional restraint …
mb2055 Sep 26, 2024
0a7fe8d
Updates changelog
mb2055 Sep 26, 2024
b8c23a3
Adds test for positional restraints on perturbed molecules
mb2055 Sep 27, 2024
e699235
Fixed typo in changelog
mb2055 Sep 27, 2024
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1 change: 1 addition & 0 deletions doc/source/changelog.rst
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Expand Up @@ -26,6 +26,7 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
* Add support for boresch restraints to PME.
* Port SOMD torsion fix to PME code.
* Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files.
* Fix issues with positionally restrained atoms in perturbable systems.


`2024.2.0 <https://github.com/openbiosim/sire/compare/2024.1.0...2024.2.0>`__ - June 2024
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8 changes: 6 additions & 2 deletions tests/convert/test_openmm_restraints.py
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Expand Up @@ -6,8 +6,12 @@
"openmm" not in sr.convert.supported_formats(),
reason="openmm support is not available",
)
def test_openmm_positional_restraints(kigaki_mols, openmm_platform):
mols = kigaki_mols
@pytest.mark.parametrize("molecules", ["kigaki_mols", "merged_ethane_methanol"])
def test_openmm_positional_restraints(molecules, openmm_platform, request):
mols = request.getfixturevalue(molecules)

if mols[0].is_perturbable():
mols = sr.morph.link_to_reference(mols)

mol = mols[0]

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3 changes: 2 additions & 1 deletion wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp
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Expand Up @@ -315,7 +315,8 @@ void _add_positional_restraints(const SireMM::PositionalRestraints &restraints,
auto ghost_nonghostff = lambda_lever.getForce<OpenMM::CustomNonbondedForce>("ghost/non-ghost", system);

std::vector<double> custom_params = {1.0, 0.0, 0.0};
std::vector<double> custom_clj_params = {0.0, 0.0, 0.0, 0.0};
// Define null parameters used to add these particles to the ghost forces (5 total)
std::vector<double> custom_clj_params = {0.0, 0.0, 0.0, 0.0, 0.0};

// we need to add all of the positions as anchor particles
for (const auto &restraint : atom_restraints)
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