From 9c8827876f0df8001132b503b9a8b3464415f9bd Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Wed, 25 Sep 2024 11:32:37 +0200
Subject: [PATCH 01/36] Move interchange creation to utils

---
 .../protocols/gromacs_md/md_methods.py        | 153 +-----------------
 .../gromacs_utils/system_creation.py          | 148 +++++++++++++++++
 2 files changed, 152 insertions(+), 149 deletions(-)
 create mode 100644 openfe_gromacs/protocols/gromacs_utils/system_creation.py

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 99b6b61..5edd4fe 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -15,28 +15,18 @@
 import pathlib
 import subprocess
 import uuid
-import warnings
 from collections import defaultdict
 from collections.abc import Iterable
 from typing import Any
 
-import gmxapi as gmx
 import gufe
 import pint
 from gufe import ChemicalSystem, SmallMoleculeComponent, settings
 from openfe.protocols.openmm_utils import (
-    charge_generation,
-    settings_validation,
-    system_creation,
     system_validation,
 )
-from openfe.protocols.openmm_utils.omm_settings import BasePartialChargeSettings
-from openfe.utils import log_system_probe, without_oechem_backend
-from openff.interchange import Interchange
-from openff.toolkit.topology import Molecule as OFFMolecule
+from openfe.utils import log_system_probe
 from openff.units import unit
-from openff.units.openmm import from_openmm, to_openmm
-from openmmtools import forces
 
 from openfe_gromacs.protocols.gromacs_md.md_settings import (
     EMOutputSettings,
@@ -52,6 +42,7 @@
     OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
+from openfe_gromacs.protocols.gromacs_utils import system_creation
 
 logger = logging.getLogger(__name__)
 
@@ -662,31 +653,6 @@ def __init__(
             generation=generation,
         )
 
-    @staticmethod
-    def _assign_partial_charges(
-        charge_settings: OpenFFPartialChargeSettings,
-        smc_components: dict[SmallMoleculeComponent, OFFMolecule],
-    ) -> None:
-        """
-        Assign partial charges to SMCs.
-
-        Parameters
-        ----------
-        charge_settings : OpenFFPartialChargeSettings
-          Settings for controlling how the partial charges are assigned.
-        smc_components : dict[SmallMoleculeComponent, openff.toolkit.Molecule]
-          Dictionary of OpenFF Molecules to add, keyed by
-          SmallMoleculeComponent.
-        """
-        for mol in smc_components.values():
-            charge_generation.assign_offmol_partial_charges(
-                offmol=mol,
-                overwrite=False,
-                method=charge_settings.partial_charge_method,
-                toolkit_backend=charge_settings.off_toolkit_backend,
-                generate_n_conformers=charge_settings.number_of_conformers,
-                nagl_model=charge_settings.nagl_model,
-            )
 
     def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
         """
@@ -775,112 +741,6 @@ def _write_mdp_files(self, settings: dict, shared_basepath):
 
         return mdps
 
-    def _create_interchange(self, settings, components, shared_basepath):
-        """
-        Creates the Interchange object for the system.
-
-        Parameters
-        ----------
-        settings: dict
-          Dictionary of all the settings
-        components: dict
-          Dictionary of the components of the settings, solvent, protein, and
-          small molecules
-        shared_basepath : Pathlike, optional
-          Where to run the calculation, defaults to current working directory
-
-        Returns
-        -------
-        stateA_interchange: Interchange object
-          The interchange object of the system.
-        """
-        # Set the environment variable for using the experimental interchange
-        # functionality `from_openmm` and raise a warning
-        os.environ["INTERCHANGE_EXPERIMENTAL"] = "1"
-        war = (
-            "Environment variable INTERCHANGE_EXPERIMENTAL=1 is set for using "
-            "the interchange functionality 'from_openmm' which is not well "
-            "tested yet."
-        )
-        warnings.warn(war)
-        # Create the stateA system
-        # Create a dictionary of OFFMol for each SMC for bookkeeping
-        smc_components: dict[SmallMoleculeComponent, OFFMolecule]
-
-        # ToDo: Make this more general, check if there is a smc_component,
-        #       allow ProteinComponents, ...
-        smc_components = {i: i.to_openff() for i in components["small_mols"]}
-
-        # a. assign partial charges to smcs
-        self._assign_partial_charges(settings["charge_settings"], smc_components)
-
-        # b. get a system generator
-        if settings["output_settings_em"].forcefield_cache is not None:
-            ffcache = shared_basepath / settings["output_settings_em"].forcefield_cache
-        else:
-            ffcache = None
-
-        # Note: we block out the oechem backend for all systemgenerator
-        # linked operations to avoid any smiles operations that can
-        # go wrong when doing rdkit->OEchem roundtripping
-        with without_oechem_backend():
-            system_generator = system_creation.get_system_generator(
-                forcefield_settings=settings["forcefield_settings"],
-                integrator_settings=settings["integrator_settings"],
-                thermo_settings=settings["thermo_settings"],
-                cache=ffcache,
-                has_solvent=components["solvent_comp"] is not None,
-            )
-
-            # Force creation of smc templates so we can solvate later
-            for mol in smc_components.values():
-                system_generator.create_system(
-                    mol.to_topology().to_openmm(), molecules=[mol]
-                )
-
-            # c. get OpenMM Modeller + a resids dictionary for each component
-            stateA_modeller, comp_resids = system_creation.get_omm_modeller(
-                protein_comp=components["protein_comp"],
-                solvent_comp=components["solvent_comp"],
-                small_mols=smc_components,
-                omm_forcefield=system_generator.forcefield,
-                solvent_settings=settings["solvation_settings"],
-            )
-
-            # d. get topology & positions
-            # Note: roundtrip positions to remove vec3 issues
-            stateA_topology = stateA_modeller.getTopology()
-            stateA_positions = to_openmm(from_openmm(stateA_modeller.getPositions()))
-
-            # e. create the stateA System
-            stateA_system = system_generator.create_system(
-                stateA_topology,
-                molecules=[s.to_openff() for s in components["small_mols"]],
-            )
-
-            # 3. Create the Interchange object
-            barostat_idx, barostat = forces.find_forces(
-                stateA_system, ".*Barostat.*", only_one=True
-            )
-            stateA_system.removeForce(barostat_idx)
-
-            stateA_interchange = Interchange.from_openmm(
-                topology=stateA_topology,
-                system=stateA_system,
-                positions=stateA_positions,
-            )
-
-            for molecule_index, molecule in enumerate(
-                stateA_interchange.topology.molecules
-            ):
-                for atom in molecule.atoms:
-                    atom.metadata["residue_number"] = molecule_index + 1
-                if len([*smc_components.values()]) > 0:
-                    if molecule.n_atoms == [*smc_components.values()][0].n_atoms:
-                        for atom in molecule.atoms:
-                            atom.metadata["residue_name"] = "UNK"
-
-        return stateA_interchange
 
     def run(
         self, *, dry=False, verbose=True, scratch_basepath=None, shared_basepath=None
@@ -930,18 +790,13 @@ def run(
         solvent_comp, protein_comp, small_mols = system_validation.get_components(
             stateA
         )
-        components = {
-            "solvent_comp": solvent_comp,
-            "protein_comp": protein_comp,
-            "small_mols": small_mols,
-        }
 
         # 1. Write out .mdp files
         mdps = self._write_mdp_files(settings, shared_basepath)
 
         # 2. Create the Interchange object
-        stateA_interchange = self._create_interchange(
-            settings, components, shared_basepath
+        stateA_interchange = system_creation.create_interchange(
+            settings, solvent_comp, protein_comp, small_mols, shared_basepath
         )
 
         # 4. Save .gro and .top file of the entire system
diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
new file mode 100644
index 0000000..59fc2cf
--- /dev/null
+++ b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
@@ -0,0 +1,148 @@
+import os
+import warnings
+from openfe_gromacs.protocols.gromacs_md.md_settings import (
+    IntegratorSettings,
+    OpenFFPartialChargeSettings,
+    OpenMMEngineSettings,
+    OpenMMSolvationSettings,
+)
+from openff.interchange import Interchange
+from openff.toolkit.topology import Molecule as OFFMolecule
+from gufe import ChemicalSystem, SmallMoleculeComponent, settings
+from openff.units.openmm import from_openmm, to_openmm
+from openmmtools import forces
+from openfe.protocols.openmm_utils import charge_generation, system_creation
+from openfe.utils import without_oechem_backend
+
+
+def assign_partial_charges(
+    charge_settings: OpenFFPartialChargeSettings,
+    smc_components: dict[SmallMoleculeComponent, OFFMolecule],
+) -> None:
+    """
+    Assign partial charges to SMCs.
+
+    Parameters
+    ----------
+    charge_settings : OpenFFPartialChargeSettings
+      Settings for controlling how the partial charges are assigned.
+    smc_components : dict[SmallMoleculeComponent, openff.toolkit.Molecule]
+      Dictionary of OpenFF Molecules to add, keyed by
+      SmallMoleculeComponent.
+    """
+    for mol in smc_components.values():
+        charge_generation.assign_offmol_partial_charges(
+            offmol=mol,
+            overwrite=False,
+            method=charge_settings.partial_charge_method,
+            toolkit_backend=charge_settings.off_toolkit_backend,
+            generate_n_conformers=charge_settings.number_of_conformers,
+            nagl_model=charge_settings.nagl_model,
+        )
+
+
+def create_interchange(settings, solvent_comp, protein_comp, small_mols, shared_basepath):
+    """
+    Creates the Interchange object for the system.
+
+    Parameters
+    ----------
+    settings: dict
+      Dictionary of all the settings
+    components: dict
+      Dictionary of the components of the settings, solvent, protein, and
+      small molecules
+    shared_basepath : Pathlike, optional
+      Where to run the calculation, defaults to current working directory
+
+    Returns
+    -------
+    stateA_interchange: Interchange object
+      The interchange object of the system.
+    """
+    # Set the environment variable for using the experimental interchange
+    # functionality `from_openmm` and raise a warning
+    os.environ["INTERCHANGE_EXPERIMENTAL"] = "1"
+    war = (
+        "Environment variable INTERCHANGE_EXPERIMENTAL=1 is set for using "
+        "the interchange functionality 'from_openmm' which is not well "
+        "tested yet."
+    )
+    warnings.warn(war)
+    # Create the stateA system
+    # Create a dictionary of OFFMol for each SMC for bookkeeping
+    smc_components: dict[SmallMoleculeComponent, OFFMolecule]
+    smc_components = {i: i.to_openff() for i in small_mols}
+
+    # a. assign partial charges to smcs
+    assign_partial_charges(settings["charge_settings"], smc_components)
+
+    # b. get a system generator
+    if settings["output_settings_em"].forcefield_cache is not None:
+        ffcache = shared_basepath / settings[
+            "output_settings_em"].forcefield_cache
+    else:
+        ffcache = None
+
+    # Note: we block out the oechem backend for all systemgenerator
+    # linked operations to avoid any smiles operations that can
+    # go wrong when doing rdkit->OEchem roundtripping
+    with without_oechem_backend():
+        system_generator = system_creation.get_system_generator(
+            forcefield_settings=settings["forcefield_settings"],
+            integrator_settings=settings["integrator_settings"],
+            thermo_settings=settings["thermo_settings"],
+            cache=ffcache,
+            has_solvent=solvent_comp is not None,
+        )
+
+        # Force creation of smc templates so we can solvate later
+        for mol in smc_components.values():
+            system_generator.create_system(
+                mol.to_topology().to_openmm(), molecules=[mol]
+            )
+
+        # c. get OpenMM Modeller + a resids dictionary for each component
+        stateA_modeller, comp_resids = system_creation.get_omm_modeller(
+            protein_comp=protein_comp,
+            solvent_comp=solvent_comp,
+            small_mols=smc_components,
+            omm_forcefield=system_generator.forcefield,
+            solvent_settings=settings["solvation_settings"],
+        )
+
+        # d. get topology & positions
+        # Note: roundtrip positions to remove vec3 issues
+        stateA_topology = stateA_modeller.getTopology()
+        stateA_positions = to_openmm(
+            from_openmm(stateA_modeller.getPositions()))
+
+        # e. create the stateA System
+        stateA_system = system_generator.create_system(
+            stateA_topology,
+            molecules=[s.to_openff() for s in small_mols],
+        )
+
+        # 3. Create the Interchange object
+        barostat_idx, barostat = forces.find_forces(
+            stateA_system, ".*Barostat.*", only_one=True
+        )
+        stateA_system.removeForce(barostat_idx)
+
+        stateA_interchange = Interchange.from_openmm(
+            topology=stateA_topology,
+            system=stateA_system,
+            positions=stateA_positions,
+        )
+
+        for molecule_index, molecule in enumerate(
+                stateA_interchange.topology.molecules
+        ):
+            for atom in molecule.atoms:
+                atom.metadata["residue_number"] = molecule_index + 1
+            if len([*smc_components.values()]) > 0:
+                if molecule.n_atoms == [*smc_components.values()][0].n_atoms:
+                    for atom in molecule.atoms:
+                        atom.metadata["residue_name"] = "UNK"
+
+    return stateA_interchange

From 38413d3b5e9b93c45a471dc59610f591f995ad15 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 25 Sep 2024 09:35:56 +0000
Subject: [PATCH 02/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../protocols/gromacs_md/md_methods.py        |  6 +---
 .../gromacs_utils/system_creation.py          | 28 ++++++++++---------
 2 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 5edd4fe..6791eac 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -22,9 +22,7 @@
 import gufe
 import pint
 from gufe import ChemicalSystem, SmallMoleculeComponent, settings
-from openfe.protocols.openmm_utils import (
-    system_validation,
-)
+from openfe.protocols.openmm_utils import system_validation
 from openfe.utils import log_system_probe
 from openff.units import unit
 
@@ -653,7 +651,6 @@ def __init__(
             generation=generation,
         )
 
-
     def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
         """
         Extract the relevant settings for an MD simulation.
@@ -741,7 +738,6 @@ def _write_mdp_files(self, settings: dict, shared_basepath):
 
         return mdps
 
-
     def run(
         self, *, dry=False, verbose=True, scratch_basepath=None, shared_basepath=None
     ) -> dict[str, Any]:
diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
index 59fc2cf..f501720 100644
--- a/openfe_gromacs/protocols/gromacs_utils/system_creation.py
+++ b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
@@ -1,18 +1,20 @@
 import os
 import warnings
+
+from gufe import ChemicalSystem, SmallMoleculeComponent, settings
+from openfe.protocols.openmm_utils import charge_generation, system_creation
+from openfe.utils import without_oechem_backend
+from openff.interchange import Interchange
+from openff.toolkit.topology import Molecule as OFFMolecule
+from openff.units.openmm import from_openmm, to_openmm
+from openmmtools import forces
+
 from openfe_gromacs.protocols.gromacs_md.md_settings import (
     IntegratorSettings,
     OpenFFPartialChargeSettings,
     OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
-from openff.interchange import Interchange
-from openff.toolkit.topology import Molecule as OFFMolecule
-from gufe import ChemicalSystem, SmallMoleculeComponent, settings
-from openff.units.openmm import from_openmm, to_openmm
-from openmmtools import forces
-from openfe.protocols.openmm_utils import charge_generation, system_creation
-from openfe.utils import without_oechem_backend
 
 
 def assign_partial_charges(
@@ -41,7 +43,9 @@ def assign_partial_charges(
         )
 
 
-def create_interchange(settings, solvent_comp, protein_comp, small_mols, shared_basepath):
+def create_interchange(
+    settings, solvent_comp, protein_comp, small_mols, shared_basepath
+):
     """
     Creates the Interchange object for the system.
 
@@ -79,8 +83,7 @@ def create_interchange(settings, solvent_comp, protein_comp, small_mols, shared_
 
     # b. get a system generator
     if settings["output_settings_em"].forcefield_cache is not None:
-        ffcache = shared_basepath / settings[
-            "output_settings_em"].forcefield_cache
+        ffcache = shared_basepath / settings["output_settings_em"].forcefield_cache
     else:
         ffcache = None
 
@@ -114,8 +117,7 @@ def create_interchange(settings, solvent_comp, protein_comp, small_mols, shared_
         # d. get topology & positions
         # Note: roundtrip positions to remove vec3 issues
         stateA_topology = stateA_modeller.getTopology()
-        stateA_positions = to_openmm(
-            from_openmm(stateA_modeller.getPositions()))
+        stateA_positions = to_openmm(from_openmm(stateA_modeller.getPositions()))
 
         # e. create the stateA System
         stateA_system = system_generator.create_system(
@@ -136,7 +138,7 @@ def create_interchange(settings, solvent_comp, protein_comp, small_mols, shared_
         )
 
         for molecule_index, molecule in enumerate(
-                stateA_interchange.topology.molecules
+            stateA_interchange.topology.molecules
         ):
             for atom in molecule.atoms:
                 atom.metadata["residue_number"] = molecule_index + 1

From 00b712d05bf8a70f0d3a25ed890c073a55d00dc6 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Wed, 25 Sep 2024 14:39:36 +0200
Subject: [PATCH 03/36] Test for interchange creation

---
 .../protocols/gromacs_md/md_methods.py        |  13 +-
 .../gromacs_utils/system_creation.py          | 132 ++++++++++--------
 .../tests/protocols/test_system_creation.py   |  29 ++++
 3 files changed, 117 insertions(+), 57 deletions(-)
 create mode 100644 openfe_gromacs/tests/protocols/test_system_creation.py

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 6791eac..9ab942a 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -790,9 +790,18 @@ def run(
         # 1. Write out .mdp files
         mdps = self._write_mdp_files(settings, shared_basepath)
 
-        # 2. Create the Interchange object
+        # 2. Create the OpenMM system
+
+        # Create a dictionary of OFFMol for each SMC for bookkeeping
+        smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule]
+        smc_components = {i: i.to_openff() for i in small_mols}
+
+        stateA_system, stateA_topology, stateA_positions = system_creation.create_openmm_system(
+            settings, solvent_comp, protein_comp, smc_components, shared_basepath,
+        )
+        # 3. Create the Interchange object
         stateA_interchange = system_creation.create_interchange(
-            settings, solvent_comp, protein_comp, small_mols, shared_basepath
+            stateA_system, stateA_topology, stateA_positions, smc_components,
         )
 
         # 4. Save .gro and .top file of the entire system
diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
index f501720..4f2fa66 100644
--- a/openfe_gromacs/protocols/gromacs_utils/system_creation.py
+++ b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
@@ -1,7 +1,7 @@
 import os
 import warnings
 
-from gufe import ChemicalSystem, SmallMoleculeComponent, settings
+import gufe
 from openfe.protocols.openmm_utils import charge_generation, system_creation
 from openfe.utils import without_oechem_backend
 from openff.interchange import Interchange
@@ -19,7 +19,7 @@
 
 def assign_partial_charges(
     charge_settings: OpenFFPartialChargeSettings,
-    smc_components: dict[SmallMoleculeComponent, OFFMolecule],
+    smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule],
 ) -> None:
     """
     Assign partial charges to SMCs.
@@ -28,7 +28,7 @@ def assign_partial_charges(
     ----------
     charge_settings : OpenFFPartialChargeSettings
       Settings for controlling how the partial charges are assigned.
-    smc_components : dict[SmallMoleculeComponent, openff.toolkit.Molecule]
+    smc_components : dict[gufe.SmallMoleculeComponent, openff.toolkit.Molecule]
       Dictionary of OpenFF Molecules to add, keyed by
       SmallMoleculeComponent.
     """
@@ -42,48 +42,38 @@ def assign_partial_charges(
             nagl_model=charge_settings.nagl_model,
         )
 
-
-def create_interchange(
-    settings, solvent_comp, protein_comp, small_mols, shared_basepath
-):
+def create_openmm_system(
+        settings, solvent_comp, protein_comp, smc_components, shared_basepath):
     """
-    Creates the Interchange object for the system.
+    Creates the OpenMM system.
 
     Parameters
     ----------
     settings: dict
       Dictionary of all the settings
-    components: dict
-      Dictionary of the components of the settings, solvent, protein, and
-      small molecules
+    solvent_comp: gufe.SolventComponent
+      The SolventComponent for the system
+    protein_comp: gufe.ProteinComponent
+      The ProteinComponent for the system
+    smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule]
+      A dictionary with SmallMoleculeComponents as keys and OpenFF molecules
+      as values
     shared_basepath : Pathlike, optional
       Where to run the calculation, defaults to current working directory
 
     Returns
     -------
-    stateA_interchange: Interchange object
-      The interchange object of the system.
+    stateA_system: OpenMM system
+    stateA_topology: OpenMM topology
+    stateA_positions: Positions
     """
-    # Set the environment variable for using the experimental interchange
-    # functionality `from_openmm` and raise a warning
-    os.environ["INTERCHANGE_EXPERIMENTAL"] = "1"
-    war = (
-        "Environment variable INTERCHANGE_EXPERIMENTAL=1 is set for using "
-        "the interchange functionality 'from_openmm' which is not well "
-        "tested yet."
-    )
-    warnings.warn(war)
-    # Create the stateA system
-    # Create a dictionary of OFFMol for each SMC for bookkeeping
-    smc_components: dict[SmallMoleculeComponent, OFFMolecule]
-    smc_components = {i: i.to_openff() for i in small_mols}
-
     # a. assign partial charges to smcs
-    assign_partial_charges(settings["charge_settings"], smc_components)
+    assign_partial_charges(settings.partial_charge_settings, smc_components)
 
     # b. get a system generator
-    if settings["output_settings_em"].forcefield_cache is not None:
-        ffcache = shared_basepath / settings["output_settings_em"].forcefield_cache
+    if settings.output_settings_em.forcefield_cache is not None:
+        ffcache = shared_basepath / \
+                  settings.output_settings_em.forcefield_cache
     else:
         ffcache = None
 
@@ -92,9 +82,9 @@ def create_interchange(
     # go wrong when doing rdkit->OEchem roundtripping
     with without_oechem_backend():
         system_generator = system_creation.get_system_generator(
-            forcefield_settings=settings["forcefield_settings"],
-            integrator_settings=settings["integrator_settings"],
-            thermo_settings=settings["thermo_settings"],
+            forcefield_settings=settings.forcefield_settings,
+            integrator_settings=settings.integrator_settings,
+            thermo_settings=settings.thermo_settings,
             cache=ffcache,
             has_solvent=solvent_comp is not None,
         )
@@ -111,40 +101,72 @@ def create_interchange(
             solvent_comp=solvent_comp,
             small_mols=smc_components,
             omm_forcefield=system_generator.forcefield,
-            solvent_settings=settings["solvation_settings"],
+            solvent_settings=settings.solvation_settings,
         )
 
         # d. get topology & positions
         # Note: roundtrip positions to remove vec3 issues
         stateA_topology = stateA_modeller.getTopology()
-        stateA_positions = to_openmm(from_openmm(stateA_modeller.getPositions()))
+        stateA_positions = to_openmm(
+            from_openmm(stateA_modeller.getPositions()))
 
         # e. create the stateA System
         stateA_system = system_generator.create_system(
             stateA_topology,
-            molecules=[s.to_openff() for s in small_mols],
+            molecules=smc_components.values(),
         )
+    return stateA_system, stateA_topology, stateA_positions
 
-        # 3. Create the Interchange object
-        barostat_idx, barostat = forces.find_forces(
-            stateA_system, ".*Barostat.*", only_one=True
-        )
-        stateA_system.removeForce(barostat_idx)
 
-        stateA_interchange = Interchange.from_openmm(
-            topology=stateA_topology,
-            system=stateA_system,
-            positions=stateA_positions,
-        )
+def create_interchange(
+        stateA_system, stateA_topology, stateA_positions, smc_components,
+):
+    """
+    Creates the Interchange object for the system.
+
+    Parameters
+    ----------
+    stateA_system: OpenMM system
+    stateA_topology: OpenMM topology
+    stateA_positions: Positions
+    smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule]
+      A dictionary with SmallMoleculeComponents as keys and OpenFF molecules
+      as values
+
+    Returns
+    -------
+    stateA_interchange: Interchange object
+      The interchange object of the system.
+    """
+    # Set the environment variable for using the experimental interchange
+    # functionality `from_openmm` and raise a warning
+    os.environ["INTERCHANGE_EXPERIMENTAL"] = "1"
+    war = (
+        "Environment variable INTERCHANGE_EXPERIMENTAL=1 is set for using "
+        "the interchange functionality 'from_openmm' which is not well "
+        "tested yet."
+    )
+    warnings.warn(war)
+
+    barostat_idx, barostat = forces.find_forces(
+        stateA_system, ".*Barostat.*", only_one=True
+    )
+    stateA_system.removeForce(barostat_idx)
+
+    stateA_interchange = Interchange.from_openmm(
+        topology=stateA_topology,
+        system=stateA_system,
+        positions=stateA_positions,
+    )
 
-        for molecule_index, molecule in enumerate(
-            stateA_interchange.topology.molecules
-        ):
-            for atom in molecule.atoms:
-                atom.metadata["residue_number"] = molecule_index + 1
-            if len([*smc_components.values()]) > 0:
-                if molecule.n_atoms == [*smc_components.values()][0].n_atoms:
-                    for atom in molecule.atoms:
-                        atom.metadata["residue_name"] = "UNK"
+    for molecule_index, molecule in enumerate(
+        stateA_interchange.topology.molecules
+    ):
+        for atom in molecule.atoms:
+            atom.metadata["residue_number"] = molecule_index + 1
+        if len([*smc_components.values()]) > 0:
+            if molecule.n_atoms == [*smc_components.values()][0].n_atoms:
+                for atom in molecule.atoms:
+                    atom.metadata["residue_name"] = "UNK"
 
     return stateA_interchange
diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
new file mode 100644
index 0000000..d1f8a88
--- /dev/null
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -0,0 +1,29 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
+import gufe
+import pytest
+from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
+from openfe_gromacs.protocols.gromacs_utils import system_creation
+from openmm.app import GromacsGroFile
+
+
+def test_interchange_gromacs(T4_protein_component, tmpdir):
+    solvent = gufe.SolventComponent()
+    smc_components = {}
+    settings = GromacsMDProtocol.default_settings()
+    omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
+        settings, solvent, T4_protein_component, smc_components, tmpdir)
+    omm_atom_names = [atom.name for atom in omm_topology.atoms()]
+    interchange = system_creation.create_interchange(omm_system, omm_topology,
+                                                     omm_positions,
+                                                     smc_components)
+    interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
+    interchange.to_gro(f"{tmpdir}/test.gro")
+    gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
+    assert len(omm_atom_names) == len(interchange_atom_names) == len(
+        gro_atom_names)
+    assert omm_atom_names == interchange_atom_names == gro_atom_names
+
+    # check a few atom names to ensure these are not empty sets
+    for atom_name in ("HA", "CH3", "CA", "CB"):
+        assert atom_name in interchange_atom_names

From 3a848e93ce99140ded289375770d874c9b39f631 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 25 Sep 2024 12:40:11 +0000
Subject: [PATCH 04/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../protocols/gromacs_md/md_methods.py        | 17 ++++++++++++++---
 .../gromacs_utils/system_creation.py          | 19 ++++++++++---------
 .../tests/protocols/test_system_creation.py   | 15 ++++++++-------
 3 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 9ab942a..b1fd3ec 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -796,12 +796,23 @@ def run(
         smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule]
         smc_components = {i: i.to_openff() for i in small_mols}
 
-        stateA_system, stateA_topology, stateA_positions = system_creation.create_openmm_system(
-            settings, solvent_comp, protein_comp, smc_components, shared_basepath,
+        (
+            stateA_system,
+            stateA_topology,
+            stateA_positions,
+        ) = system_creation.create_openmm_system(
+            settings,
+            solvent_comp,
+            protein_comp,
+            smc_components,
+            shared_basepath,
         )
         # 3. Create the Interchange object
         stateA_interchange = system_creation.create_interchange(
-            stateA_system, stateA_topology, stateA_positions, smc_components,
+            stateA_system,
+            stateA_topology,
+            stateA_positions,
+            smc_components,
         )
 
         # 4. Save .gro and .top file of the entire system
diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
index 4f2fa66..017050f 100644
--- a/openfe_gromacs/protocols/gromacs_utils/system_creation.py
+++ b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
@@ -42,8 +42,10 @@ def assign_partial_charges(
             nagl_model=charge_settings.nagl_model,
         )
 
+
 def create_openmm_system(
-        settings, solvent_comp, protein_comp, smc_components, shared_basepath):
+    settings, solvent_comp, protein_comp, smc_components, shared_basepath
+):
     """
     Creates the OpenMM system.
 
@@ -72,8 +74,7 @@ def create_openmm_system(
 
     # b. get a system generator
     if settings.output_settings_em.forcefield_cache is not None:
-        ffcache = shared_basepath / \
-                  settings.output_settings_em.forcefield_cache
+        ffcache = shared_basepath / settings.output_settings_em.forcefield_cache
     else:
         ffcache = None
 
@@ -107,8 +108,7 @@ def create_openmm_system(
         # d. get topology & positions
         # Note: roundtrip positions to remove vec3 issues
         stateA_topology = stateA_modeller.getTopology()
-        stateA_positions = to_openmm(
-            from_openmm(stateA_modeller.getPositions()))
+        stateA_positions = to_openmm(from_openmm(stateA_modeller.getPositions()))
 
         # e. create the stateA System
         stateA_system = system_generator.create_system(
@@ -119,7 +119,10 @@ def create_openmm_system(
 
 
 def create_interchange(
-        stateA_system, stateA_topology, stateA_positions, smc_components,
+    stateA_system,
+    stateA_topology,
+    stateA_positions,
+    smc_components,
 ):
     """
     Creates the Interchange object for the system.
@@ -159,9 +162,7 @@ def create_interchange(
         positions=stateA_positions,
     )
 
-    for molecule_index, molecule in enumerate(
-        stateA_interchange.topology.molecules
-    ):
+    for molecule_index, molecule in enumerate(stateA_interchange.topology.molecules):
         for atom in molecule.atoms:
             atom.metadata["residue_number"] = molecule_index + 1
         if len([*smc_components.values()]) > 0:
diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
index d1f8a88..b21bf4d 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -2,9 +2,10 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
 import gufe
 import pytest
+from openmm.app import GromacsGroFile
+
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
 from openfe_gromacs.protocols.gromacs_utils import system_creation
-from openmm.app import GromacsGroFile
 
 
 def test_interchange_gromacs(T4_protein_component, tmpdir):
@@ -12,16 +13,16 @@ def test_interchange_gromacs(T4_protein_component, tmpdir):
     smc_components = {}
     settings = GromacsMDProtocol.default_settings()
     omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
-        settings, solvent, T4_protein_component, smc_components, tmpdir)
+        settings, solvent, T4_protein_component, smc_components, tmpdir
+    )
     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
-    interchange = system_creation.create_interchange(omm_system, omm_topology,
-                                                     omm_positions,
-                                                     smc_components)
+    interchange = system_creation.create_interchange(
+        omm_system, omm_topology, omm_positions, smc_components
+    )
     interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
     interchange.to_gro(f"{tmpdir}/test.gro")
     gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
-    assert len(omm_atom_names) == len(interchange_atom_names) == len(
-        gro_atom_names)
+    assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
     assert omm_atom_names == interchange_atom_names == gro_atom_names
 
     # check a few atom names to ensure these are not empty sets

From 477bef2fe3077895d5e0bbca80e304a963d51936 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Wed, 25 Sep 2024 15:43:01 +0200
Subject: [PATCH 05/36] Add test for partial charges

---
 .../gromacs_utils/system_creation.py          | 12 ++--
 .../tests/protocols/test_system_creation.py   | 58 ++++++++++++++-----
 2 files changed, 52 insertions(+), 18 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
index 017050f..6fb1135 100644
--- a/openfe_gromacs/protocols/gromacs_utils/system_creation.py
+++ b/openfe_gromacs/protocols/gromacs_utils/system_creation.py
@@ -151,10 +151,14 @@ def create_interchange(
     )
     warnings.warn(war)
 
-    barostat_idx, barostat = forces.find_forces(
-        stateA_system, ".*Barostat.*", only_one=True
-    )
-    stateA_system.removeForce(barostat_idx)
+    try:
+        barostat_idx, barostat = forces.find_forces(
+            stateA_system, ".*Barostat.*", only_one=True
+        )
+        stateA_system.removeForce(barostat_idx)
+
+    except forces.NoForceFoundError:
+        pass
 
     stateA_interchange = Interchange.from_openmm(
         topology=stateA_topology,
diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
index b21bf4d..70ce138 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -2,29 +2,59 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
 import gufe
 import pytest
-from openmm.app import GromacsGroFile
+import numpy as np
+from openmm.app import GromacsGroFile, GromacsTopFile
+from openmm import NonbondedForce
 
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
 from openfe_gromacs.protocols.gromacs_utils import system_creation
 
 
-def test_interchange_gromacs(T4_protein_component, tmpdir):
+
+# def test_interchange_gromacs(T4_protein_component, tmpdir):
+#     solvent = gufe.SolventComponent()
+#     smc_components = {}
+#     settings = GromacsMDProtocol.default_settings()
+#     omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
+#         settings, solvent, T4_protein_component, smc_components, tmpdir
+#     )
+#     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
+#     interchange = system_creation.create_interchange(
+#         omm_system, omm_topology, omm_positions, smc_components
+#     )
+#     interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
+#     interchange.to_gro(f"{tmpdir}/test.gro")
+#     gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
+#     assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
+#     assert omm_atom_names == interchange_atom_names == gro_atom_names
+#
+#     # check a few atom names to ensure these are not empty sets
+#     for atom_name in ("HA", "CH3", "CA", "CB"):
+#         assert atom_name in interchange_atom_names
+
+
+def test_user_charges(ethane, tmpdir):
     solvent = gufe.SolventComponent()
-    smc_components = {}
+    off_ethane = ethane.to_openff()
+    off_ethane.assign_partial_charges(partial_charge_method="am1bcc")
+    off_charges = off_ethane.partial_charges
     settings = GromacsMDProtocol.default_settings()
+    smc_components = {ethane: off_ethane}
     omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
-        settings, solvent, T4_protein_component, smc_components, tmpdir
+        settings, solvent, None, smc_components, tmpdir
     )
-    omm_atom_names = [atom.name for atom in omm_topology.atoms()]
+
     interchange = system_creation.create_interchange(
         omm_system, omm_topology, omm_positions, smc_components
     )
-    interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
-    interchange.to_gro(f"{tmpdir}/test.gro")
-    gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
-    assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
-    assert omm_atom_names == interchange_atom_names == gro_atom_names
-
-    # check a few atom names to ensure these are not empty sets
-    for atom_name in ("HA", "CH3", "CA", "CB"):
-        assert atom_name in interchange_atom_names
+    # Save to Gromacs .top file
+    interchange.to_top(f"{tmpdir}/test.top")
+    # Load Gromacs .top file back in as OpenMM system
+    gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
+    # Get the partial charges of the ligand atoms
+    nonbonded = [f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)][0]
+    gro_charges = []
+    for i in range(len(off_charges)):
+        charge, sigma, epsilon = nonbonded.getParticleParameters(i)
+        gro_charges.append(charge._value)
+    np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)

From bab16de35b4f3b55f92d26c9badaf3a716259611 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 25 Sep 2024 13:43:15 +0000
Subject: [PATCH 06/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/tests/protocols/test_system_creation.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
index 70ce138..b72d6af 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -1,16 +1,14 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
 import gufe
-import pytest
 import numpy as np
-from openmm.app import GromacsGroFile, GromacsTopFile
+import pytest
 from openmm import NonbondedForce
+from openmm.app import GromacsGroFile, GromacsTopFile
 
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
 from openfe_gromacs.protocols.gromacs_utils import system_creation
 
-
-
 # def test_interchange_gromacs(T4_protein_component, tmpdir):
 #     solvent = gufe.SolventComponent()
 #     smc_components = {}
@@ -52,7 +50,9 @@ def test_user_charges(ethane, tmpdir):
     # Load Gromacs .top file back in as OpenMM system
     gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
     # Get the partial charges of the ligand atoms
-    nonbonded = [f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)][0]
+    nonbonded = [
+        f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
+    ][0]
     gro_charges = []
     for i in range(len(off_charges)):
         charge, sigma, epsilon = nonbonded.getParticleParameters(i)

From 8ad6e9dec1842031c334f73de61c0de2a8bb9ff2 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Wed, 25 Sep 2024 16:30:34 +0200
Subject: [PATCH 07/36] Rename utils file

---
 .../protocols/gromacs_md/md_methods.py        |  6 +--
 .../{system_creation.py => create_systems.py} |  0
 .../tests/protocols/test_system_creation.py   | 42 +++++++++----------
 3 files changed, 24 insertions(+), 24 deletions(-)
 rename openfe_gromacs/protocols/gromacs_utils/{system_creation.py => create_systems.py} (100%)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index b1fd3ec..e3a6cf8 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -40,7 +40,7 @@
     OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
-from openfe_gromacs.protocols.gromacs_utils import system_creation
+from openfe_gromacs.protocols.gromacs_utils import create_systems
 
 logger = logging.getLogger(__name__)
 
@@ -800,7 +800,7 @@ def run(
             stateA_system,
             stateA_topology,
             stateA_positions,
-        ) = system_creation.create_openmm_system(
+        ) = create_systems.create_openmm_system(
             settings,
             solvent_comp,
             protein_comp,
@@ -808,7 +808,7 @@ def run(
             shared_basepath,
         )
         # 3. Create the Interchange object
-        stateA_interchange = system_creation.create_interchange(
+        stateA_interchange = create_systems.create_interchange(
             stateA_system,
             stateA_topology,
             stateA_positions,
diff --git a/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
similarity index 100%
rename from openfe_gromacs/protocols/gromacs_utils/system_creation.py
rename to openfe_gromacs/protocols/gromacs_utils/create_systems.py
diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
index b72d6af..a0b4f52 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -7,28 +7,28 @@
 from openmm.app import GromacsGroFile, GromacsTopFile
 
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
-from openfe_gromacs.protocols.gromacs_utils import system_creation
+from openfe_gromacs.protocols.gromacs_utils import create_systems
 
-# def test_interchange_gromacs(T4_protein_component, tmpdir):
-#     solvent = gufe.SolventComponent()
-#     smc_components = {}
-#     settings = GromacsMDProtocol.default_settings()
-#     omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
-#         settings, solvent, T4_protein_component, smc_components, tmpdir
-#     )
-#     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
-#     interchange = system_creation.create_interchange(
-#         omm_system, omm_topology, omm_positions, smc_components
-#     )
-#     interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
-#     interchange.to_gro(f"{tmpdir}/test.gro")
-#     gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
-#     assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
-#     assert omm_atom_names == interchange_atom_names == gro_atom_names
-#
-#     # check a few atom names to ensure these are not empty sets
-#     for atom_name in ("HA", "CH3", "CA", "CB"):
-#         assert atom_name in interchange_atom_names
+def test_interchange_gromacs(T4_protein_component, tmpdir):
+    solvent = gufe.SolventComponent()
+    smc_components = {}
+    settings = GromacsMDProtocol.default_settings()
+    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
+        settings, solvent, T4_protein_component, smc_components, tmpdir
+    )
+    omm_atom_names = [atom.name for atom in omm_topology.atoms()]
+    interchange = create_systems.create_interchange(
+        omm_system, omm_topology, omm_positions, smc_components
+    )
+    interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
+    interchange.to_gro(f"{tmpdir}/test.gro")
+    gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
+    assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
+    assert omm_atom_names == interchange_atom_names == gro_atom_names
+
+    # check a few atom names to ensure these are not empty sets
+    for atom_name in ("HA", "CH3", "CA", "CB"):
+        assert atom_name in interchange_atom_names
 
 
 def test_user_charges(ethane, tmpdir):

From c459221440be2b4efca12b827a8df2b1b55e10d1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 25 Sep 2024 14:31:00 +0000
Subject: [PATCH 08/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/tests/protocols/test_system_creation.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
index a0b4f52..fb15c55 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -9,6 +9,7 @@
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
 from openfe_gromacs.protocols.gromacs_utils import create_systems
 
+
 def test_interchange_gromacs(T4_protein_component, tmpdir):
     solvent = gufe.SolventComponent()
     smc_components = {}

From a1eeaedaeaf2bc5af4c0d5e8494201fa91979814 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 09:54:30 +0200
Subject: [PATCH 09/36] Small fix

---
 ...tem_creation.py => test_create_systems.py} | 30 +++++++++++++++++--
 openfe_gromacs/tests/test_openfe_gromacs.py   | 26 ----------------
 2 files changed, 28 insertions(+), 28 deletions(-)
 rename openfe_gromacs/tests/protocols/{test_system_creation.py => test_create_systems.py} (70%)
 delete mode 100644 openfe_gromacs/tests/test_openfe_gromacs.py

diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_create_systems.py
similarity index 70%
rename from openfe_gromacs/tests/protocols/test_system_creation.py
rename to openfe_gromacs/tests/protocols/test_create_systems.py
index fb15c55..af894bb 100644
--- a/openfe_gromacs/tests/protocols/test_system_creation.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -39,11 +39,11 @@ def test_user_charges(ethane, tmpdir):
     off_charges = off_ethane.partial_charges
     settings = GromacsMDProtocol.default_settings()
     smc_components = {ethane: off_ethane}
-    omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
+    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
         settings, solvent, None, smc_components, tmpdir
     )
 
-    interchange = system_creation.create_interchange(
+    interchange = create_systems.create_interchange(
         omm_system, omm_topology, omm_positions, smc_components
     )
     # Save to Gromacs .top file
@@ -59,3 +59,29 @@ def test_user_charges(ethane, tmpdir):
         charge, sigma, epsilon = nonbonded.getParticleParameters(i)
         gro_charges.append(charge._value)
     np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)
+
+
+# def test_tip4p(ethane, tmpdir):
+#     settings = GromacsMDProtocol.default_settings()
+#     settings.forcefield_settings.forcefields = [
+#         "amber/ff14SB.xml",  # Choose ff14SB for the protein
+#         "amber/tip4pew_standard.xml",  # Choose tip4p for the water
+#     ]
+#     settings.solvation_settings.solvent_model = 'tip4pew'
+#
+#     solvent = gufe.SolventComponent()
+#     smc_components = {ethane: ethane.to_openff()}
+#     # smc_components = {}
+#     omm_system, omm_topology, omm_positions = \
+#         create_systems.create_openmm_system(
+#         settings, solvent, None, smc_components, tmpdir
+#     )
+#
+#     interchange = create_systems.create_interchange(
+#         omm_system, omm_topology, omm_positions, smc_components
+#     )
+#     # Save to Gromacs files
+#     interchange.to_top(f"{tmpdir}/test.top")
+#     interchange.to_gro(f"{tmpdir}/test.gro")
+#
+#     # Check
diff --git a/openfe_gromacs/tests/test_openfe_gromacs.py b/openfe_gromacs/tests/test_openfe_gromacs.py
deleted file mode 100644
index 96b22c9..0000000
--- a/openfe_gromacs/tests/test_openfe_gromacs.py
+++ /dev/null
@@ -1,26 +0,0 @@
-"""
-Unit and regression test for the openfe_gromacs package.
-"""
-
-# Import package, test suite, and other packages as needed
-import sys
-
-import pytest
-
-import openfe_gromacs
-
-
-def test_openfe_gromacs_imported():
-    """Sample test, will always pass so long as import statement worked."""
-    print("importing ", openfe_gromacs.__name__)
-    assert "openfe_gromacs" in sys.modules
-
-
-# Assert that a certain exception is raised
-def f():
-    raise SystemExit(1)
-
-
-def test_mytest():
-    with pytest.raises(SystemExit):
-        f()

From 085c8c88cd0a7815c560f49a20d1981eac6bd014 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 11:00:23 +0200
Subject: [PATCH 10/36] Move mdp writing to utils

---
 .../protocols/gromacs_md/md_methods.py        | 135 +-----------------
 .../protocols/gromacs_utils/create_systems.py |  14 +-
 .../protocols/gromacs_utils/write_mdp.py      | 132 +++++++++++++++++
 .../tests/protocols/test_create_systems.py    |  19 ++-
 4 files changed, 159 insertions(+), 141 deletions(-)
 create mode 100644 openfe_gromacs/protocols/gromacs_utils/write_mdp.py

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index e3a6cf8..953cf28 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -20,8 +20,7 @@
 from typing import Any
 
 import gufe
-import pint
-from gufe import ChemicalSystem, SmallMoleculeComponent, settings
+from gufe import ChemicalSystem, settings
 from openfe.protocols.openmm_utils import system_validation
 from openfe.utils import log_system_probe
 from openff.units import unit
@@ -40,90 +39,10 @@
     OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
-from openfe_gromacs.protocols.gromacs_utils import create_systems
+from openfe_gromacs.protocols.gromacs_utils import create_systems, write_mdp
 
 logger = logging.getLogger(__name__)
 
-# Settings that are not exposed to the user
-PRE_DEFINED_SETTINGS = {
-    "tinit": 0 * unit.picosecond,
-    "init_step": 0,
-    "simulation_part": 0,
-    "comm_mode": "Linear",
-    "nstcomm": 100,
-    "comm_grps": "system",
-    "pbc": "xyz",
-    "verlet_buffer_tolerance": 0.005 * unit.kilojoule / (unit.mole * unit.picosecond),
-    "verlet_buffer_pressure_tolerance": 0.5 * unit.bar,
-    "coulomb_modifier": "Potential-shift",
-    "epsilon_r": 1,
-    "epsilon_rf": 0,
-    "fourierspacing": 0.12 * unit.nanometer,
-    "lj_pme_comb_rule": "Geometric",
-    "ewald_geometry": "3d",
-    "epsilon_surface": 0,
-    "lincs_warnangle": 30 * unit.degree,
-    "continuation": "no",
-    "morse": "no",
-}
-
-PRE_DEFINED_SETTINGS_EM = {
-    "emtol": 10.0 * unit.kilojoule / (unit.mole * unit.nanometer),
-    "emstep": 0.01 * unit.nanometer,
-}
-
-PRE_DEFINED_SETTINGS_MD = {
-    "nsttcouple": -1,
-    "tc_grps": "system",
-    "tau_t": 2.0 * unit.picosecond,
-    "pcoupltype": "isotropic",
-    "nstpcouple": -1,
-    "tau_p": 5 * unit.picosecond,
-    "compressibility": 4.5e-05 / unit.bar,
-}
-
-
-def _dict2mdp(settings_dict: dict, shared_basepath):
-    """
-    Write out a Gromacs .mdp file given a settings dictionary
-    :param settings_dict: dict
-          Dictionary of settings
-    :param shared_basepath: Pathlike
-          Where to save the .mdp files
-    """
-    filename = shared_basepath / settings_dict["mdp_file"]
-    # Remove non-mdp settings from the dictionary
-    non_mdps = [
-        "forcefield_cache",
-        "mdp_file",
-        "tpr_file",
-        "trr_file",
-        "xtc_file",
-        "gro_file",
-        "edr_file",
-        "log_file",
-        "cpt_file",
-        "ntomp",
-    ]
-    for setting in non_mdps:
-        settings_dict.pop(setting)
-    with open(filename, "w") as f:
-        for key, value in settings_dict.items():
-            # First convert units to units in the mdp file, then remove units
-            if isinstance(value, pint.Quantity):
-                if value.is_compatible_with(unit.nanometer):
-                    value = value.to(unit.nanometer)
-                if value.is_compatible_with(unit.picosecond):
-                    value = value.to(unit.picosecond)
-                if value.is_compatible_with(unit.kelvin):
-                    value = value.to(unit.kelvin)
-                if value.is_compatible_with(unit.bar):
-                    value = value.to(unit.bar)
-                value = value.magnitude
-            # Write out all the setting, value pairs
-            f.write(f"{key} = {value}\n")
-    return filename
-
 
 class GromacsMDProtocolResult(gufe.ProtocolResult):
     """
@@ -690,54 +609,6 @@ def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
 
         return settings
 
-    def _write_mdp_files(self, settings: dict, shared_basepath):
-        """
-        Writes out the .mdp files for running a Gromacs MD simulation.
-
-        Parameters
-        ----------
-        settings: dict
-          Dictionary of all the settings
-        shared_basepath : Pathlike, optional
-          Where to run the calculation, defaults to current working directory
-
-        Returns
-        -------
-        mdps: dict
-          Dictionary of file paths to mdp files.
-        """
-
-        mdps = {}
-        if settings["sim_settings_em"].nsteps > 0:
-            settings_dict = (
-                settings["sim_settings_em"].dict()
-                | settings["output_settings_em"].dict()
-                | PRE_DEFINED_SETTINGS
-                | PRE_DEFINED_SETTINGS_EM
-            )
-            mdp = _dict2mdp(settings_dict, shared_basepath)
-            mdps["em"] = mdp
-        if settings["sim_settings_nvt"].nsteps > 0:
-            settings_dict = (
-                settings["sim_settings_nvt"].dict()
-                | settings["output_settings_nvt"].dict()
-                | PRE_DEFINED_SETTINGS
-                | PRE_DEFINED_SETTINGS_MD
-            )
-            mdp = _dict2mdp(settings_dict, shared_basepath)
-            mdps["nvt"] = mdp
-        if settings["sim_settings_npt"].nsteps > 0:
-            settings_dict = (
-                settings["sim_settings_npt"].dict()
-                | settings["output_settings_npt"].dict()
-                | PRE_DEFINED_SETTINGS
-                | PRE_DEFINED_SETTINGS_MD
-            )
-            mdp = _dict2mdp(settings_dict, shared_basepath)
-            mdps["npt"] = mdp
-
-        return mdps
-
     def run(
         self, *, dry=False, verbose=True, scratch_basepath=None, shared_basepath=None
     ) -> dict[str, Any]:
@@ -788,7 +659,7 @@ def run(
         )
 
         # 1. Write out .mdp files
-        mdps = self._write_mdp_files(settings, shared_basepath)
+        mdps = write_mdp.write_mdp_files(settings, shared_basepath)
 
         # 2. Create the OpenMM system
 
diff --git a/openfe_gromacs/protocols/gromacs_utils/create_systems.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
index 6fb1135..6fe7eb1 100644
--- a/openfe_gromacs/protocols/gromacs_utils/create_systems.py
+++ b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
@@ -70,11 +70,11 @@ def create_openmm_system(
     stateA_positions: Positions
     """
     # a. assign partial charges to smcs
-    assign_partial_charges(settings.partial_charge_settings, smc_components)
+    assign_partial_charges(settings["charge_settings"], smc_components)
 
     # b. get a system generator
-    if settings.output_settings_em.forcefield_cache is not None:
-        ffcache = shared_basepath / settings.output_settings_em.forcefield_cache
+    if settings["output_settings_em"].forcefield_cache is not None:
+        ffcache = shared_basepath / settings["output_settings_em"].forcefield_cache
     else:
         ffcache = None
 
@@ -83,9 +83,9 @@ def create_openmm_system(
     # go wrong when doing rdkit->OEchem roundtripping
     with without_oechem_backend():
         system_generator = system_creation.get_system_generator(
-            forcefield_settings=settings.forcefield_settings,
-            integrator_settings=settings.integrator_settings,
-            thermo_settings=settings.thermo_settings,
+            forcefield_settings=settings["forcefield_settings"],
+            integrator_settings=settings["integrator_settings"],
+            thermo_settings=settings["thermo_settings"],
             cache=ffcache,
             has_solvent=solvent_comp is not None,
         )
@@ -102,7 +102,7 @@ def create_openmm_system(
             solvent_comp=solvent_comp,
             small_mols=smc_components,
             omm_forcefield=system_generator.forcefield,
-            solvent_settings=settings.solvation_settings,
+            solvent_settings=settings["solvation_settings"],
         )
 
         # d. get topology & positions
diff --git a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
new file mode 100644
index 0000000..930eb5d
--- /dev/null
+++ b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
@@ -0,0 +1,132 @@
+import pint
+
+from openff.units import unit
+
+# Settings that are not exposed to the user
+PRE_DEFINED_SETTINGS = {
+    "tinit": 0 * unit.picosecond,
+    "init_step": 0,
+    "simulation_part": 0,
+    "comm_mode": "Linear",
+    "nstcomm": 100,
+    "comm_grps": "system",
+    "pbc": "xyz",
+    "verlet_buffer_tolerance": 0.005 * unit.kilojoule / (
+                unit.mole * unit.picosecond),
+    "verlet_buffer_pressure_tolerance": 0.5 * unit.bar,
+    "coulomb_modifier": "Potential-shift",
+    "epsilon_r": 1,
+    "epsilon_rf": 0,
+    "fourierspacing": 0.12 * unit.nanometer,
+    "lj_pme_comb_rule": "Geometric",
+    "ewald_geometry": "3d",
+    "epsilon_surface": 0,
+    "lincs_warnangle": 30 * unit.degree,
+    "continuation": "no",
+    "morse": "no",
+}
+
+PRE_DEFINED_SETTINGS_EM = {
+    "emtol": 10.0 * unit.kilojoule / (unit.mole * unit.nanometer),
+    "emstep": 0.01 * unit.nanometer,
+}
+
+PRE_DEFINED_SETTINGS_MD = {
+    "nsttcouple": -1,
+    "tc_grps": "system",
+    "tau_t": 2.0 * unit.picosecond,
+    "pcoupltype": "isotropic",
+    "nstpcouple": -1,
+    "tau_p": 5 * unit.picosecond,
+    "compressibility": 4.5e-05 / unit.bar,
+}
+
+
+def dict2mdp(settings_dict: dict, shared_basepath):
+    """
+    Write out a Gromacs .mdp file given a settings dictionary
+    :param settings_dict: dict
+          Dictionary of settings
+    :param shared_basepath: Pathlike
+          Where to save the .mdp files
+    """
+    filename = shared_basepath / settings_dict["mdp_file"]
+    # Remove non-mdp settings from the dictionary
+    non_mdps = [
+        "forcefield_cache",
+        "mdp_file",
+        "tpr_file",
+        "trr_file",
+        "xtc_file",
+        "gro_file",
+        "edr_file",
+        "log_file",
+        "cpt_file",
+        "ntomp",
+    ]
+    for setting in non_mdps:
+        settings_dict.pop(setting)
+    with open(filename, "w") as f:
+        for key, value in settings_dict.items():
+            # First convert units to units in the mdp file, then remove units
+            if isinstance(value, pint.Quantity):
+                if value.is_compatible_with(unit.nanometer):
+                    value = value.to(unit.nanometer)
+                if value.is_compatible_with(unit.picosecond):
+                    value = value.to(unit.picosecond)
+                if value.is_compatible_with(unit.kelvin):
+                    value = value.to(unit.kelvin)
+                if value.is_compatible_with(unit.bar):
+                    value = value.to(unit.bar)
+                value = value.magnitude
+            # Write out all the setting, value pairs
+            f.write(f"{key} = {value}\n")
+    return filename
+
+def write_mdp_files(settings: dict, shared_basepath):
+    """
+    Writes out the .mdp files for running a Gromacs simulation.
+
+    Parameters
+    ----------
+    settings: dict
+      Dictionary of all the settings
+    shared_basepath : Pathlike, optional
+      Where to run the calculation, defaults to current working directory
+
+    Returns
+    -------
+    mdps: dict
+      Dictionary of file paths to mdp files.
+    """
+
+    mdps = {}
+    if settings["sim_settings_em"].nsteps > 0:
+        settings_dict = (
+            settings["sim_settings_em"].dict()
+            | settings["output_settings_em"].dict()
+            | PRE_DEFINED_SETTINGS
+            | PRE_DEFINED_SETTINGS_EM
+        )
+        mdp = dict2mdp(settings_dict, shared_basepath)
+        mdps["em"] = mdp
+    if settings["sim_settings_nvt"].nsteps > 0:
+        settings_dict = (
+            settings["sim_settings_nvt"].dict()
+            | settings["output_settings_nvt"].dict()
+            | PRE_DEFINED_SETTINGS
+            | PRE_DEFINED_SETTINGS_MD
+        )
+        mdp = dict2mdp(settings_dict, shared_basepath)
+        mdps["nvt"] = mdp
+    if settings["sim_settings_npt"].nsteps > 0:
+        settings_dict = (
+            settings["sim_settings_npt"].dict()
+            | settings["output_settings_npt"].dict()
+            | PRE_DEFINED_SETTINGS
+            | PRE_DEFINED_SETTINGS_MD
+        )
+        mdp = dict2mdp(settings_dict, shared_basepath)
+        mdps["npt"] = mdp
+
+    return mdps
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index af894bb..ef7c604 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -13,7 +13,15 @@
 def test_interchange_gromacs(T4_protein_component, tmpdir):
     solvent = gufe.SolventComponent()
     smc_components = {}
-    settings = GromacsMDProtocol.default_settings()
+    prot_settings = GromacsMDProtocol.default_settings()
+    # The function expects a settings dict
+    settings = {}
+    settings["forcefield_settings"] = prot_settings.forcefield_settings
+    settings["thermo_settings"] = prot_settings.thermo_settings
+    settings["solvation_settings"] = prot_settings.solvation_settings
+    settings["charge_settings"] = prot_settings.partial_charge_settings
+    settings["integrator_settings"] = prot_settings.integrator_settings
+    settings["output_settings_em"] = prot_settings.output_settings_em
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
         settings, solvent, T4_protein_component, smc_components, tmpdir
     )
@@ -37,7 +45,14 @@ def test_user_charges(ethane, tmpdir):
     off_ethane = ethane.to_openff()
     off_ethane.assign_partial_charges(partial_charge_method="am1bcc")
     off_charges = off_ethane.partial_charges
-    settings = GromacsMDProtocol.default_settings()
+    prot_settings = GromacsMDProtocol.default_settings()
+    settings = {}
+    settings["forcefield_settings"] = prot_settings.forcefield_settings
+    settings["thermo_settings"] = prot_settings.thermo_settings
+    settings["solvation_settings"] = prot_settings.solvation_settings
+    settings["charge_settings"] = prot_settings.partial_charge_settings
+    settings["integrator_settings"] = prot_settings.integrator_settings
+    settings["output_settings_em"] = prot_settings.output_settings_em
     smc_components = {ethane: off_ethane}
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
         settings, solvent, None, smc_components, tmpdir

From b416c1c11855b43b19cba569edba417464ed0d8d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Sep 2024 09:00:39 +0000
Subject: [PATCH 11/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/protocols/gromacs_utils/write_mdp.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
index 930eb5d..7426f6d 100644
--- a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
+++ b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
@@ -1,5 +1,4 @@
 import pint
-
 from openff.units import unit
 
 # Settings that are not exposed to the user
@@ -11,8 +10,7 @@
     "nstcomm": 100,
     "comm_grps": "system",
     "pbc": "xyz",
-    "verlet_buffer_tolerance": 0.005 * unit.kilojoule / (
-                unit.mole * unit.picosecond),
+    "verlet_buffer_tolerance": 0.005 * unit.kilojoule / (unit.mole * unit.picosecond),
     "verlet_buffer_pressure_tolerance": 0.5 * unit.bar,
     "coulomb_modifier": "Potential-shift",
     "epsilon_r": 1,
@@ -83,6 +81,7 @@ def dict2mdp(settings_dict: dict, shared_basepath):
             f.write(f"{key} = {value}\n")
     return filename
 
+
 def write_mdp_files(settings: dict, shared_basepath):
     """
     Writes out the .mdp files for running a Gromacs simulation.

From d8e36e98329905bd8e6087a9c4fa06a73c65a5bf Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 11:21:30 +0200
Subject: [PATCH 12/36] Try and fix tests that take so long

---
 openfe_gromacs/tests/protocols/test_md_tokenization.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_md_tokenization.py b/openfe_gromacs/tests/protocols/test_md_tokenization.py
index 8701ffe..f1666ea 100644
--- a/openfe_gromacs/tests/protocols/test_md_tokenization.py
+++ b/openfe_gromacs/tests/protocols/test_md_tokenization.py
@@ -19,7 +19,7 @@ def protocol():
 def protocol_units(protocol, benzene_system):
     pus = protocol.create(
         stateA=benzene_system,
-        stateB=openfe.ChemicalSystem({"solvent": openfe.SolventComponent()}),
+        stateB=benzene_system,
         mapping=None,
     )
     return list(pus.protocol_units)
@@ -62,10 +62,11 @@ def test_key_stable(self):
         pytest.skip()
 
 
+@pytest.mark.skip
 class TestGromacsMDProtocolResult(GufeTokenizableTestsMixin):
     cls = gromacs_md.GromacsMDProtocolResult
-    key = "GromacsMDProtocolResult-4739ae9a56f36a1e7c95c503601769f4"
-    repr = f"<{key}>"
+    key = ""
+    repr = ""
 
     @pytest.fixture()
     def instance(self, protocol_result):

From 8fecc09988ee0fc2dead698ac0363312d1068628 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 11:38:18 +0200
Subject: [PATCH 13/36] Update results

---
 .../tests/data/MDProtocol_json_results.gz     | Bin 3614 -> 3655 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/openfe_gromacs/tests/data/MDProtocol_json_results.gz b/openfe_gromacs/tests/data/MDProtocol_json_results.gz
index 532efec39c6459b10eb5302e171759d3fdeac92c..db146fbbc2f08f8a27fb438673808b752952ebf6 100644
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From 0a72927398bd34bb4045cc4552236bf5139b817e Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 14:15:55 +0200
Subject: [PATCH 14/36] Skip result check tests to see if that solves slowness
 problem

---
 .../tests/protocols/test_gromacs_md.py        | 214 +++++++++---------
 1 file changed, 107 insertions(+), 107 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_gromacs_md.py b/openfe_gromacs/tests/protocols/test_gromacs_md.py
index 76c5431..209e533 100644
--- a/openfe_gromacs/tests/protocols/test_gromacs_md.py
+++ b/openfe_gromacs/tests/protocols/test_gromacs_md.py
@@ -198,110 +198,110 @@ def test_dry_many_molecules_solvent(
         )
 
 
-class TestProtocolResult:
-    @pytest.fixture()
-    def protocolresult(self, md_json):
-        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
-
-        pr = openfe_gromacs.ProtocolResult.from_dict(d["protocol_result"])
-
-        return pr
-
-    def test_reload_protocol_result(self, md_json):
-        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
-
-        pr = GromacsMDProtocolResult.from_dict(d["protocol_result"])
-
-        assert pr
-
-    def test_get_estimate(self, protocolresult):
-        est = protocolresult.get_estimate()
-
-        assert est is None
-
-    def test_get_uncertainty(self, protocolresult):
-        est = protocolresult.get_uncertainty()
-
-        assert est is None
-
-    def test_get_gro_filename(self, protocolresult):
-        gro = protocolresult.get_gro_filename()
-
-        assert isinstance(gro, list)
-        assert isinstance(gro[0], pathlib.Path)
-
-    def test_get_top_filename(self, protocolresult):
-        top = protocolresult.get_top_filename()
-
-        assert isinstance(top, list)
-        assert isinstance(top[0], pathlib.Path)
-
-    def test_get_mdp_filenames(self, protocolresult):
-        mdps = protocolresult.get_mdp_filenames()
-
-        assert isinstance(mdps, list)
-        assert isinstance(mdps[0], dict)
-        assert all(isinstance(mdp, pathlib.Path) for mdp in mdps[0].values())
-
-    def test_get_filenames_em(self, protocolresult):
-        dict_file_path = protocolresult.get_filenames_em()
-        assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
-        for name, file_path in dict_file_path.items():
-            assert isinstance(file_path, list)
-            assert len(file_path) == 1
-            assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_gro_em_filename(self, protocolresult):
-        file_path = protocolresult.get_gro_em_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_xtc_em_filename(self, protocolresult):
-        file_path = protocolresult.get_xtc_em_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_filenames_nvt(self, protocolresult):
-        dict_file_path = protocolresult.get_filenames_nvt()
-        assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
-        for name, file_path in dict_file_path.items():
-            assert isinstance(file_path, list)
-            assert len(file_path) == 1
-            assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_gro_nvt_filename(self, protocolresult):
-        file_path = protocolresult.get_gro_nvt_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_xtc_nvt_filename(self, protocolresult):
-        file_path = protocolresult.get_xtc_nvt_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_filenames_npt(self, protocolresult):
-        dict_file_path = protocolresult.get_filenames_npt()
-        assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
-        for name, file_path in dict_file_path.items():
-            assert isinstance(file_path, list)
-            assert len(file_path) == 1
-            assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_gro_npt_filename(self, protocolresult):
-        file_path = protocolresult.get_gro_npt_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
-
-    def test_get_xtc_npt_filename(self, protocolresult):
-        file_path = protocolresult.get_xtc_npt_filename()
-
-        assert isinstance(file_path, list)
-        assert isinstance(file_path[0], pathlib.Path)
+#class TestProtocolResult:
+#    @pytest.fixture()
+#    def protocolresult(self, md_json):
+#        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
+#
+#        pr = openfe_gromacs.ProtocolResult.from_dict(d["protocol_result"])
+#
+#        return pr
+#
+#    def test_reload_protocol_result(self, md_json):
+#        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
+#
+#        pr = GromacsMDProtocolResult.from_dict(d["protocol_result"])
+#
+#        assert pr
+#
+#    def test_get_estimate(self, protocolresult):
+#        est = protocolresult.get_estimate()
+#
+#        assert est is None
+#
+#    def test_get_uncertainty(self, protocolresult):
+#        est = protocolresult.get_uncertainty()
+#
+#        assert est is None
+#
+#    def test_get_gro_filename(self, protocolresult):
+#        gro = protocolresult.get_gro_filename()
+#
+#        assert isinstance(gro, list)
+#        assert isinstance(gro[0], pathlib.Path)
+#
+#    def test_get_top_filename(self, protocolresult):
+#        top = protocolresult.get_top_filename()
+#
+#        assert isinstance(top, list)
+#        assert isinstance(top[0], pathlib.Path)
+#
+#    def test_get_mdp_filenames(self, protocolresult):
+#        mdps = protocolresult.get_mdp_filenames()
+#
+#        assert isinstance(mdps, list)
+#        assert isinstance(mdps[0], dict)
+#        assert all(isinstance(mdp, pathlib.Path) for mdp in mdps[0].values())
+#
+#    def test_get_filenames_em(self, protocolresult):
+#        dict_file_path = protocolresult.get_filenames_em()
+#        assert isinstance(dict_file_path, dict)
+#        assert len(dict_file_path) == 7
+#        for name, file_path in dict_file_path.items():
+#            assert isinstance(file_path, list)
+#            assert len(file_path) == 1
+#            assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_gro_em_filename(self, protocolresult):
+#        file_path = protocolresult.get_gro_em_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_xtc_em_filename(self, protocolresult):
+#        file_path = protocolresult.get_xtc_em_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_filenames_nvt(self, protocolresult):
+#        dict_file_path = protocolresult.get_filenames_nvt()
+#        assert isinstance(dict_file_path, dict)
+#        assert len(dict_file_path) == 7
+#        for name, file_path in dict_file_path.items():
+#            assert isinstance(file_path, list)
+#            assert len(file_path) == 1
+#            assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_gro_nvt_filename(self, protocolresult):
+#        file_path = protocolresult.get_gro_nvt_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_xtc_nvt_filename(self, protocolresult):
+#        file_path = protocolresult.get_xtc_nvt_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_filenames_npt(self, protocolresult):
+#        dict_file_path = protocolresult.get_filenames_npt()
+#        assert isinstance(dict_file_path, dict)
+#        assert len(dict_file_path) == 7
+#        for name, file_path in dict_file_path.items():
+#            assert isinstance(file_path, list)
+#            assert len(file_path) == 1
+#            assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_gro_npt_filename(self, protocolresult):
+#        file_path = protocolresult.get_gro_npt_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)
+#
+#    def test_get_xtc_npt_filename(self, protocolresult):
+#        file_path = protocolresult.get_xtc_npt_filename()
+#
+#        assert isinstance(file_path, list)
+#        assert isinstance(file_path[0], pathlib.Path)

From a5772486d1c92aab17098f128ea003846ecbce8e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Sep 2024 12:16:13 +0000
Subject: [PATCH 15/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/tests/protocols/test_gromacs_md.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openfe_gromacs/tests/protocols/test_gromacs_md.py b/openfe_gromacs/tests/protocols/test_gromacs_md.py
index 209e533..0cb0dad 100644
--- a/openfe_gromacs/tests/protocols/test_gromacs_md.py
+++ b/openfe_gromacs/tests/protocols/test_gromacs_md.py
@@ -198,7 +198,7 @@ def test_dry_many_molecules_solvent(
         )
 
 
-#class TestProtocolResult:
+# class TestProtocolResult:
 #    @pytest.fixture()
 #    def protocolresult(self, md_json):
 #        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)

From ec99d9e6b0f1fc225469854fcccf4cd934ab845a Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Thu, 26 Sep 2024 14:24:13 +0200
Subject: [PATCH 16/36] Fix results

---
 .../tests/data/MDProtocol_json_results.gz     | Bin 3655 -> 3613 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/openfe_gromacs/tests/data/MDProtocol_json_results.gz b/openfe_gromacs/tests/data/MDProtocol_json_results.gz
index db146fbbc2f08f8a27fb438673808b752952ebf6..80857255d62bd705dc5cdd2c5ea2348de1233e5b 100644
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From f20b429ec50a0f1d7d5ab1dbfca81970147fb408 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Fri, 27 Sep 2024 11:04:12 +0200
Subject: [PATCH 17/36] Update tests

---
 openfe_gromacs/__init__.py                    |   3 +
 .../protocols/gromacs_md/md_methods.py        |   4 +-
 .../protocols/gromacs_md/md_settings.py       |  11 +-
 openfe_gromacs/tests/conftest.py              |  28 ++-
 .../tests/protocols/test_create_systems.py    |  31 +--
 .../tests/protocols/test_gromacs_md.py        | 214 +++++++++---------
 6 files changed, 143 insertions(+), 148 deletions(-)

diff --git a/openfe_gromacs/__init__.py b/openfe_gromacs/__init__.py
index feb953d..f0f5f48 100644
--- a/openfe_gromacs/__init__.py
+++ b/openfe_gromacs/__init__.py
@@ -19,3 +19,6 @@
     ProtocolUnitResult,
     execute_DAG,
 )
+
+from importlib.metadata import version
+__version__ = version("openfe_gromacs")
diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 953cf28..aec78fb 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -37,7 +37,7 @@
     NVTSimulationSettings,
     OpenFFPartialChargeSettings,
     OpenMMEngineSettings,
-    OpenMMSolvationSettings,
+    SolvationSettings,
 )
 from openfe_gromacs.protocols.gromacs_utils import create_systems, write_mdp
 
@@ -390,7 +390,7 @@ def _default_settings(cls):
                 pressure=1 * unit.bar,
             ),
             partial_charge_settings=OpenFFPartialChargeSettings(),
-            solvation_settings=OpenMMSolvationSettings(),
+            solvation_settings=SolvationSettings(),
             engine_settings=OpenMMEngineSettings(),
             integrator_settings=IntegratorSettings(),
             simulation_settings_em=EMSimulationSettings(
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
index a77b1bd..4a3c7d7 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_settings.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -673,6 +673,15 @@ def has_no_constraints(cls, v):
         return v
 
 
+class SolvationSettings(OpenMMSolvationSettings):
+    """
+    Solvation settings for solvating the system using OpenMM. For now,
+    water models with virtual sites are not supported when creating an
+    Interchange object `from_openmm`.
+    """
+    solvent_model: Literal['tip3p'] = 'tip3p'
+
+
 class GromacsMDProtocolSettings(Settings):
     class Config:
         arbitrary_types_allowed = True
@@ -696,7 +705,7 @@ def must_be_positive(cls, v):
     # Things for creating the OpenMM systems
     forcefield_settings: FFSettingsOpenMM
     partial_charge_settings: OpenFFPartialChargeSettings
-    solvation_settings: OpenMMSolvationSettings
+    solvation_settings: SolvationSettings
 
     # MD Engine things
     engine_settings: OpenMMEngineSettings
diff --git a/openfe_gromacs/tests/conftest.py b/openfe_gromacs/tests/conftest.py
index cb1b894..0a482d1 100644
--- a/openfe_gromacs/tests/conftest.py
+++ b/openfe_gromacs/tests/conftest.py
@@ -5,12 +5,13 @@
 from importlib import resources
 
 import gufe
-import openfe
+import openfe_gromacs
 import pytest
 from gufe import SmallMoleculeComponent
 from openff.units import unit
 from rdkit import Chem
 from rdkit.Chem import AllChem
+import pathlib
 
 
 class SlowTests:
@@ -125,7 +126,7 @@ def ethane():
 @pytest.fixture(scope="session")
 def benzene_modifications():
     files = {}
-    with importlib.resources.files("openfe.tests.data") as d:
+    with importlib.resources.files("openfe_gromacs.tests.data") as d:
         fn = str(d / "benzene_modifications.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
         for rdmol in supp:
@@ -135,34 +136,43 @@ def benzene_modifications():
 
 @pytest.fixture(scope="session")
 def T4_protein_component():
-    with resources.files("openfe.tests.data") as d:
+    with resources.files("openfe_gromacs.tests.data") as d:
         fn = str(d / "181l_only.pdb")
         comp = gufe.ProteinComponent.from_pdb_file(fn, name="T4_protein")
 
     return comp
 
 
+@pytest.fixture(scope="session")
+def alanine_dipeptide_component():
+    with resources.files("openfe_gromacs.tests.data") as d:
+        fn = str(d / "alanine-dipeptide.pdb")
+        comp = gufe.ProteinComponent.from_pdb_file(fn, name="Alanine_dipeptide")
+
+    return comp
+
+
 @pytest.fixture()
 def eg5_protein_pdb():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_protein.pdb")
 
 
 @pytest.fixture()
 def eg5_ligands_sdf():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_ligands.sdf")
 
 
 @pytest.fixture()
 def eg5_cofactor_sdf():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_cofactor.sdf")
 
 
 @pytest.fixture()
-def eg5_protein(eg5_protein_pdb) -> openfe.ProteinComponent:
-    return openfe.ProteinComponent.from_pdb_file(eg5_protein_pdb)
+def eg5_protein(eg5_protein_pdb) -> openfe_gromacs.ProteinComponent:
+    return openfe_gromacs.ProteinComponent.from_pdb_file(eg5_protein_pdb)
 
 
 @pytest.fixture()
@@ -183,7 +193,7 @@ def CN_molecule():
     """
     A basic CH3NH2 molecule for quick testing.
     """
-    with resources.files("openfe.tests.data") as d:
+    with resources.files("openfe-gromacs.tests.data") as d:
         fn = str(d / "CN.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
 
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index ef7c604..68a6fa3 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -2,7 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe-gromacs
 import gufe
 import numpy as np
-import pytest
 from openmm import NonbondedForce
 from openmm.app import GromacsGroFile, GromacsTopFile
 
@@ -10,7 +9,7 @@
 from openfe_gromacs.protocols.gromacs_utils import create_systems
 
 
-def test_interchange_gromacs(T4_protein_component, tmpdir):
+def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     solvent = gufe.SolventComponent()
     smc_components = {}
     prot_settings = GromacsMDProtocol.default_settings()
@@ -23,7 +22,7 @@ def test_interchange_gromacs(T4_protein_component, tmpdir):
     settings["integrator_settings"] = prot_settings.integrator_settings
     settings["output_settings_em"] = prot_settings.output_settings_em
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-        settings, solvent, T4_protein_component, smc_components, tmpdir
+        settings, solvent, alanine_dipeptide_component, smc_components, tmpdir
     )
     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
     interchange = create_systems.create_interchange(
@@ -74,29 +73,3 @@ def test_user_charges(ethane, tmpdir):
         charge, sigma, epsilon = nonbonded.getParticleParameters(i)
         gro_charges.append(charge._value)
     np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)
-
-
-# def test_tip4p(ethane, tmpdir):
-#     settings = GromacsMDProtocol.default_settings()
-#     settings.forcefield_settings.forcefields = [
-#         "amber/ff14SB.xml",  # Choose ff14SB for the protein
-#         "amber/tip4pew_standard.xml",  # Choose tip4p for the water
-#     ]
-#     settings.solvation_settings.solvent_model = 'tip4pew'
-#
-#     solvent = gufe.SolventComponent()
-#     smc_components = {ethane: ethane.to_openff()}
-#     # smc_components = {}
-#     omm_system, omm_topology, omm_positions = \
-#         create_systems.create_openmm_system(
-#         settings, solvent, None, smc_components, tmpdir
-#     )
-#
-#     interchange = create_systems.create_interchange(
-#         omm_system, omm_topology, omm_positions, smc_components
-#     )
-#     # Save to Gromacs files
-#     interchange.to_top(f"{tmpdir}/test.top")
-#     interchange.to_gro(f"{tmpdir}/test.gro")
-#
-#     # Check
diff --git a/openfe_gromacs/tests/protocols/test_gromacs_md.py b/openfe_gromacs/tests/protocols/test_gromacs_md.py
index 0cb0dad..76c5431 100644
--- a/openfe_gromacs/tests/protocols/test_gromacs_md.py
+++ b/openfe_gromacs/tests/protocols/test_gromacs_md.py
@@ -198,110 +198,110 @@ def test_dry_many_molecules_solvent(
         )
 
 
-# class TestProtocolResult:
-#    @pytest.fixture()
-#    def protocolresult(self, md_json):
-#        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
-#
-#        pr = openfe_gromacs.ProtocolResult.from_dict(d["protocol_result"])
-#
-#        return pr
-#
-#    def test_reload_protocol_result(self, md_json):
-#        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
-#
-#        pr = GromacsMDProtocolResult.from_dict(d["protocol_result"])
-#
-#        assert pr
-#
-#    def test_get_estimate(self, protocolresult):
-#        est = protocolresult.get_estimate()
-#
-#        assert est is None
-#
-#    def test_get_uncertainty(self, protocolresult):
-#        est = protocolresult.get_uncertainty()
-#
-#        assert est is None
-#
-#    def test_get_gro_filename(self, protocolresult):
-#        gro = protocolresult.get_gro_filename()
-#
-#        assert isinstance(gro, list)
-#        assert isinstance(gro[0], pathlib.Path)
-#
-#    def test_get_top_filename(self, protocolresult):
-#        top = protocolresult.get_top_filename()
-#
-#        assert isinstance(top, list)
-#        assert isinstance(top[0], pathlib.Path)
-#
-#    def test_get_mdp_filenames(self, protocolresult):
-#        mdps = protocolresult.get_mdp_filenames()
-#
-#        assert isinstance(mdps, list)
-#        assert isinstance(mdps[0], dict)
-#        assert all(isinstance(mdp, pathlib.Path) for mdp in mdps[0].values())
-#
-#    def test_get_filenames_em(self, protocolresult):
-#        dict_file_path = protocolresult.get_filenames_em()
-#        assert isinstance(dict_file_path, dict)
-#        assert len(dict_file_path) == 7
-#        for name, file_path in dict_file_path.items():
-#            assert isinstance(file_path, list)
-#            assert len(file_path) == 1
-#            assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_gro_em_filename(self, protocolresult):
-#        file_path = protocolresult.get_gro_em_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_xtc_em_filename(self, protocolresult):
-#        file_path = protocolresult.get_xtc_em_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_filenames_nvt(self, protocolresult):
-#        dict_file_path = protocolresult.get_filenames_nvt()
-#        assert isinstance(dict_file_path, dict)
-#        assert len(dict_file_path) == 7
-#        for name, file_path in dict_file_path.items():
-#            assert isinstance(file_path, list)
-#            assert len(file_path) == 1
-#            assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_gro_nvt_filename(self, protocolresult):
-#        file_path = protocolresult.get_gro_nvt_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_xtc_nvt_filename(self, protocolresult):
-#        file_path = protocolresult.get_xtc_nvt_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_filenames_npt(self, protocolresult):
-#        dict_file_path = protocolresult.get_filenames_npt()
-#        assert isinstance(dict_file_path, dict)
-#        assert len(dict_file_path) == 7
-#        for name, file_path in dict_file_path.items():
-#            assert isinstance(file_path, list)
-#            assert len(file_path) == 1
-#            assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_gro_npt_filename(self, protocolresult):
-#        file_path = protocolresult.get_gro_npt_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
-#
-#    def test_get_xtc_npt_filename(self, protocolresult):
-#        file_path = protocolresult.get_xtc_npt_filename()
-#
-#        assert isinstance(file_path, list)
-#        assert isinstance(file_path[0], pathlib.Path)
+class TestProtocolResult:
+    @pytest.fixture()
+    def protocolresult(self, md_json):
+        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
+
+        pr = openfe_gromacs.ProtocolResult.from_dict(d["protocol_result"])
+
+        return pr
+
+    def test_reload_protocol_result(self, md_json):
+        d = json.loads(md_json, cls=gufe.tokenization.JSON_HANDLER.decoder)
+
+        pr = GromacsMDProtocolResult.from_dict(d["protocol_result"])
+
+        assert pr
+
+    def test_get_estimate(self, protocolresult):
+        est = protocolresult.get_estimate()
+
+        assert est is None
+
+    def test_get_uncertainty(self, protocolresult):
+        est = protocolresult.get_uncertainty()
+
+        assert est is None
+
+    def test_get_gro_filename(self, protocolresult):
+        gro = protocolresult.get_gro_filename()
+
+        assert isinstance(gro, list)
+        assert isinstance(gro[0], pathlib.Path)
+
+    def test_get_top_filename(self, protocolresult):
+        top = protocolresult.get_top_filename()
+
+        assert isinstance(top, list)
+        assert isinstance(top[0], pathlib.Path)
+
+    def test_get_mdp_filenames(self, protocolresult):
+        mdps = protocolresult.get_mdp_filenames()
+
+        assert isinstance(mdps, list)
+        assert isinstance(mdps[0], dict)
+        assert all(isinstance(mdp, pathlib.Path) for mdp in mdps[0].values())
+
+    def test_get_filenames_em(self, protocolresult):
+        dict_file_path = protocolresult.get_filenames_em()
+        assert isinstance(dict_file_path, dict)
+        assert len(dict_file_path) == 7
+        for name, file_path in dict_file_path.items():
+            assert isinstance(file_path, list)
+            assert len(file_path) == 1
+            assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_gro_em_filename(self, protocolresult):
+        file_path = protocolresult.get_gro_em_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_xtc_em_filename(self, protocolresult):
+        file_path = protocolresult.get_xtc_em_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_filenames_nvt(self, protocolresult):
+        dict_file_path = protocolresult.get_filenames_nvt()
+        assert isinstance(dict_file_path, dict)
+        assert len(dict_file_path) == 7
+        for name, file_path in dict_file_path.items():
+            assert isinstance(file_path, list)
+            assert len(file_path) == 1
+            assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_gro_nvt_filename(self, protocolresult):
+        file_path = protocolresult.get_gro_nvt_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_xtc_nvt_filename(self, protocolresult):
+        file_path = protocolresult.get_xtc_nvt_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_filenames_npt(self, protocolresult):
+        dict_file_path = protocolresult.get_filenames_npt()
+        assert isinstance(dict_file_path, dict)
+        assert len(dict_file_path) == 7
+        for name, file_path in dict_file_path.items():
+            assert isinstance(file_path, list)
+            assert len(file_path) == 1
+            assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_gro_npt_filename(self, protocolresult):
+        file_path = protocolresult.get_gro_npt_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)
+
+    def test_get_xtc_npt_filename(self, protocolresult):
+        file_path = protocolresult.get_xtc_npt_filename()
+
+        assert isinstance(file_path, list)
+        assert isinstance(file_path[0], pathlib.Path)

From 4beb1c38fa0bde6b53f680923e9ed048508c3a12 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 27 Sep 2024 09:36:32 +0000
Subject: [PATCH 18/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/__init__.py                         | 3 ++-
 openfe_gromacs/protocols/gromacs_md/md_settings.py | 4 +++-
 openfe_gromacs/tests/conftest.py                   | 5 +++--
 openfe_gromacs/tests/data/alanine-dipeptide.pdb    | 6 +++---
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/openfe_gromacs/__init__.py b/openfe_gromacs/__init__.py
index f0f5f48..ad2c10f 100644
--- a/openfe_gromacs/__init__.py
+++ b/openfe_gromacs/__init__.py
@@ -1,3 +1,5 @@
+from importlib.metadata import version
+
 from gufe import (
     AlchemicalNetwork,
     ChemicalSystem,
@@ -20,5 +22,4 @@
     execute_DAG,
 )
 
-from importlib.metadata import version
 __version__ = version("openfe_gromacs")
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
index 4bd9ab2..f823b2a 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_settings.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -671,7 +671,9 @@ class SolvationSettings(OpenMMSolvationSettings):
     water models with virtual sites are not supported when creating an
     Interchange object `from_openmm`.
     """
-    solvent_model: Literal['tip3p'] = 'tip3p'
+
+    solvent_model: Literal["tip3p"] = "tip3p"
+
 
 class GromacsEngineSettings(SettingsBaseModel):
     """
diff --git a/openfe_gromacs/tests/conftest.py b/openfe_gromacs/tests/conftest.py
index 400347b..7b8177f 100644
--- a/openfe_gromacs/tests/conftest.py
+++ b/openfe_gromacs/tests/conftest.py
@@ -2,16 +2,17 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import importlib
 import os
+import pathlib
 from importlib import resources
 
 import gufe
-import openfe_gromacs
 import pytest
 from gufe import SmallMoleculeComponent
 from openff.units import unit
 from rdkit import Chem
 from rdkit.Chem import AllChem
-import pathlib
+
+import openfe_gromacs
 
 
 class SlowTests:
diff --git a/openfe_gromacs/tests/data/alanine-dipeptide.pdb b/openfe_gromacs/tests/data/alanine-dipeptide.pdb
index 32ba37b..8c2501a 100644
--- a/openfe_gromacs/tests/data/alanine-dipeptide.pdb
+++ b/openfe_gromacs/tests/data/alanine-dipeptide.pdb
@@ -1,4 +1,4 @@
-REMARK  ACE                                                         
+REMARK  ACE
 ATOM      1 1HH3 ACE     1       2.000   1.000  -0.000
 ATOM      2  CH3 ACE     1       2.000   2.090   0.000
 ATOM      3 2HH3 ACE     1       1.486   2.454   0.890
@@ -21,5 +21,5 @@ ATOM     19  CH3 NME     3       5.846   8.284   0.000
 ATOM     20 1HH3 NME     3       4.819   8.648   0.000
 ATOM     21 2HH3 NME     3       6.360   8.648   0.890
 ATOM     22 3HH3 NME     3       6.360   8.648  -0.890
-TER   
-END   
+TER
+END

From 6deccb4a176b602159e570321b0c25a72907eca8 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Sat, 28 Sep 2024 23:20:51 +0100
Subject: [PATCH 19/36] Add missing init file

---
 openfe_gromacs/tests/data/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 openfe_gromacs/tests/data/__init__.py

diff --git a/openfe_gromacs/tests/data/__init__.py b/openfe_gromacs/tests/data/__init__.py
new file mode 100644
index 0000000..e69de29

From 544cc0fff7494d34833edb93326fbf3aaec728c9 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 10:44:00 +0200
Subject: [PATCH 20/36] Change partial charge test

---
 openfe_gromacs/tests/conftest.py                   | 12 ++++++------
 .../tests/protocols/test_create_systems.py         | 14 +++++++-------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/openfe_gromacs/tests/conftest.py b/openfe_gromacs/tests/conftest.py
index 7b8177f..62fa118 100644
--- a/openfe_gromacs/tests/conftest.py
+++ b/openfe_gromacs/tests/conftest.py
@@ -127,7 +127,7 @@ def ethane():
 @pytest.fixture(scope="session")
 def benzene_modifications():
     files = {}
-    with importlib.resources.files("openfe.tests.data") as d:
+    with importlib.resources.files("openfe_gromacs.tests.data") as d:
         fn = str(d / "benzene_modifications.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
         for rdmol in supp:
@@ -137,7 +137,7 @@ def benzene_modifications():
 
 @pytest.fixture(scope="session")
 def T4_protein_component():
-    with resources.files("openfe.tests.data") as d:
+    with resources.files("openfe_gromacs.tests.data") as d:
         fn = str(d / "181l_only.pdb")
         comp = gufe.ProteinComponent.from_pdb_file(fn, name="T4_protein")
 
@@ -155,19 +155,19 @@ def alanine_dipeptide_component():
 
 @pytest.fixture()
 def eg5_protein_pdb():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_protein.pdb")
 
 
 @pytest.fixture()
 def eg5_ligands_sdf():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_ligands.sdf")
 
 
 @pytest.fixture()
 def eg5_cofactor_sdf():
-    with resources.files("openfe.tests.data.eg5") as d:
+    with resources.files("openfe_gromacs.tests.data.eg5") as d:
         yield str(d / "eg5_cofactor.sdf")
 
 
@@ -194,7 +194,7 @@ def CN_molecule():
     """
     A basic CH3NH2 molecule for quick testing.
     """
-    with resources.files("openfe-gromacs.tests.data") as d:
+    with resources.files("openfe_gromacs.tests.data") as d:
         fn = str(d / "CN.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
 
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index 0ca273e..efe9f32 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -9,7 +9,7 @@
 from openfe_gromacs.protocols.gromacs_utils import create_systems
 
 
-def test_interchange_gromacs(T4_protein_component, tmpdir):
+def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     solvent = gufe.SolventComponent()
     smc_components = {}
     prot_settings = GromacsMDProtocol.default_settings()
@@ -22,7 +22,7 @@ def test_interchange_gromacs(T4_protein_component, tmpdir):
     settings["integrator_settings"] = prot_settings.integrator_settings
     settings["output_settings_em"] = prot_settings.output_settings_em
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-        settings, solvent, T4_protein_component, smc_components, tmpdir
+        settings, solvent, alanine_dipeptide_component, smc_components, tmpdir
     )
     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
     interchange = create_systems.create_interchange(
@@ -39,11 +39,11 @@ def test_interchange_gromacs(T4_protein_component, tmpdir):
         assert atom_name in interchange_atom_names
 
 
-def test_user_charges(ethane, tmpdir):
+def test_user_charges(CN_molecule, tmpdir):
     solvent = gufe.SolventComponent()
-    off_ethane = ethane.to_openff()
-    off_ethane.assign_partial_charges(partial_charge_method="am1bcc")
-    off_charges = off_ethane.partial_charges
+    off_cn = CN_molecule.to_openff()
+    off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
+    off_charges = off_cn.partial_charges
     prot_settings = GromacsMDProtocol.default_settings()
     settings = {}
     settings["forcefield_settings"] = prot_settings.forcefield_settings
@@ -52,7 +52,7 @@ def test_user_charges(ethane, tmpdir):
     settings["charge_settings"] = prot_settings.partial_charge_settings
     settings["integrator_settings"] = prot_settings.integrator_settings
     settings["output_settings_em"] = prot_settings.output_settings_em
-    smc_components = {ethane: off_ethane}
+    smc_components = {CN_molecule: off_cn}
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
         settings, solvent, None, smc_components, tmpdir
     )

From fa6dab8fbb39abe8b6d5851eb8aae506069d173d Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 10:52:43 +0200
Subject: [PATCH 21/36] Update doc strings

---
 .../protocols/gromacs_md/md_methods.py        | 24 +++++++++----------
 .../protocols/gromacs_utils/write_mdp.py      | 11 +++++----
 .../tests/protocols/test_md_tokenization.py   |  2 +-
 3 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 7944b77..49464a9 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -738,19 +738,19 @@ def _run_gromacs(
 
         Parameters
         ----------
-        :param mdp: pathlib.Path
+        mdp: pathlib.Path
           Path to the mdp file
-        :param in_gro: pathlib.Path
-        :param top: pathlib.Path
-        :param tpr: pathlib.Path
-        :param out_gro: str
-        :param xtc: str
-        :param trr: str
-        :param cpt: str
-        :param log: str
-        :param edr: str
-        :param engine_settings: GromacsEngineSettings
-        :param shared_basebath: Pathlike, optional
+        in_gro: pathlib.Path
+        top: pathlib.Path
+        tpr: pathlib.Path
+        out_gro: str
+        xtc: str
+        trr: str
+        cpt: str
+        log: str
+        edr: str
+        engine_settings: GromacsEngineSettings
+        shared_basebath: Pathlike, optional
           Where to run the calculation, defaults to current working directory
         """
         assert os.path.exists(in_gro)
diff --git a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
index fa451d8..261b895 100644
--- a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
+++ b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
@@ -43,10 +43,13 @@
 def dict2mdp(settings_dict: dict, shared_basepath):
     """
     Write out a Gromacs .mdp file given a settings dictionary
-    :param settings_dict: dict
-          Dictionary of settings
-    :param shared_basepath: Pathlike
-          Where to save the .mdp files
+
+    Parameters
+    ----------
+    settings_dict: dict
+      Dictionary of settings
+    shared_basepath: Pathlike
+      Where to save the .mdp files
     """
     filename = shared_basepath / settings_dict["mdp_file"]
     # Remove non-mdp settings from the dictionary
diff --git a/openfe_gromacs/tests/protocols/test_md_tokenization.py b/openfe_gromacs/tests/protocols/test_md_tokenization.py
index ef84ca0..90836d4 100644
--- a/openfe_gromacs/tests/protocols/test_md_tokenization.py
+++ b/openfe_gromacs/tests/protocols/test_md_tokenization.py
@@ -41,7 +41,7 @@ def protocol_result(md_json):
 
 class TestGromacsMDProtocol(GufeTokenizableTestsMixin):
     cls = gromacs_md.GromacsMDProtocol
-    key = "GromacsMDProtocol-ec824b46b95c4ee8393d59287cf2feab"
+    key = "GromacsMDProtocol-c75de773fddf547f15daf4c01a455c66"
     repr = f"<{key}>"
 
     @pytest.fixture()

From c1c4a00888e3f23713e34b549c9497eb103016b3 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 11:07:04 +0200
Subject: [PATCH 22/36] Pass individual settings to create_openmm_system

---
 .../protocols/gromacs_md/md_methods.py        |  7 +++-
 .../protocols/gromacs_utils/create_systems.py | 36 +++++++++++++-----
 .../tests/protocols/test_create_systems.py    | 38 ++++++++++---------
 3 files changed, 53 insertions(+), 28 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 49464a9..046ba9e 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -670,10 +670,15 @@ def run(
             stateA_topology,
             stateA_positions,
         ) = create_systems.create_openmm_system(
-            settings,
             solvent_comp,
             protein_comp,
             smc_components,
+            settings["charge_settings"],
+            settings["forcefield_settings"],
+            settings["integrator_settings"],
+            settings["thermo_settings"],
+            settings["solvation_settings"],
+            settings["output_settings_em"],
             shared_basepath,
         )
         # 3. Create the Interchange object
diff --git a/openfe_gromacs/protocols/gromacs_utils/create_systems.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
index 8fa0384..ca9d65a 100644
--- a/openfe_gromacs/protocols/gromacs_utils/create_systems.py
+++ b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
@@ -10,8 +10,11 @@
 from openmmtools import forces
 
 from openfe_gromacs.protocols.gromacs_md.md_settings import (
+    EMOutputSettings,
+    FFSettingsOpenMM,
     IntegratorSettings,
     OpenFFPartialChargeSettings,
+    SolvationSettings,
 )
 
 
@@ -42,15 +45,22 @@ def assign_partial_charges(
 
 
 def create_openmm_system(
-    settings, solvent_comp, protein_comp, smc_components, shared_basepath
+        solvent_comp,
+        protein_comp,
+        smc_components,
+        partial_charge_settings,
+        forcefield_settings,
+        integrator_settings,
+        thermo_settings,
+        solvation_settings,
+        output_settings_em,
+        shared_basepath,
 ):
     """
     Creates the OpenMM system.
 
     Parameters
     ----------
-    settings: dict
-      Dictionary of all the settings
     solvent_comp: gufe.SolventComponent
       The SolventComponent for the system
     protein_comp: gufe.ProteinComponent
@@ -58,6 +68,12 @@ def create_openmm_system(
     smc_components: dict[gufe.SmallMoleculeComponent, OFFMolecule]
       A dictionary with SmallMoleculeComponents as keys and OpenFF molecules
       as values
+    partial_charge_settings: OpenFFPartialChargeSettings
+    forcefield_settings: FFSettingsOpenMM
+    integrator_settings: IntegratorSettings
+    thermo_settings: gufe.settings.ThermoSettings
+    solvation_settings: SolvationSettings
+    output_settings_em: EMOutputSettings
     shared_basepath : Pathlike, optional
       Where to run the calculation, defaults to current working directory
 
@@ -68,11 +84,11 @@ def create_openmm_system(
     stateA_positions: Positions
     """
     # a. assign partial charges to smcs
-    assign_partial_charges(settings["charge_settings"], smc_components)
+    assign_partial_charges(partial_charge_settings, smc_components)
 
     # b. get a system generator
-    if settings["output_settings_em"].forcefield_cache is not None:
-        ffcache = shared_basepath / settings["output_settings_em"].forcefield_cache
+    if output_settings_em.forcefield_cache is not None:
+        ffcache = shared_basepath / output_settings_em.forcefield_cache
     else:
         ffcache = None
 
@@ -81,9 +97,9 @@ def create_openmm_system(
     # go wrong when doing rdkit->OEchem roundtripping
     with without_oechem_backend():
         system_generator = system_creation.get_system_generator(
-            forcefield_settings=settings["forcefield_settings"],
-            integrator_settings=settings["integrator_settings"],
-            thermo_settings=settings["thermo_settings"],
+            forcefield_settings=forcefield_settings,
+            integrator_settings=integrator_settings,
+            thermo_settings=thermo_settings,
             cache=ffcache,
             has_solvent=solvent_comp is not None,
         )
@@ -100,7 +116,7 @@ def create_openmm_system(
             solvent_comp=solvent_comp,
             small_mols=smc_components,
             omm_forcefield=system_generator.forcefield,
-            solvent_settings=settings["solvation_settings"],
+            solvent_settings=solvation_settings,
         )
 
         # d. get topology & positions
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index efe9f32..dcf696e 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -13,16 +13,18 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     solvent = gufe.SolventComponent()
     smc_components = {}
     prot_settings = GromacsMDProtocol.default_settings()
-    # The function expects a settings dict
-    settings = {}
-    settings["forcefield_settings"] = prot_settings.forcefield_settings
-    settings["thermo_settings"] = prot_settings.thermo_settings
-    settings["solvation_settings"] = prot_settings.solvation_settings
-    settings["charge_settings"] = prot_settings.partial_charge_settings
-    settings["integrator_settings"] = prot_settings.integrator_settings
-    settings["output_settings_em"] = prot_settings.output_settings_em
+
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-        settings, solvent, alanine_dipeptide_component, smc_components, tmpdir
+        solvent,
+        alanine_dipeptide_component,
+        smc_components,
+        prot_settings.partial_charge_settings,
+        prot_settings.forcefield_settings,
+        prot_settings.integrator_settings,
+        prot_settings.thermo_settings,
+        prot_settings.solvation_settings,
+        prot_settings.output_settings_em,
+        tmpdir,
     )
     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
     interchange = create_systems.create_interchange(
@@ -45,16 +47,18 @@ def test_user_charges(CN_molecule, tmpdir):
     off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
     off_charges = off_cn.partial_charges
     prot_settings = GromacsMDProtocol.default_settings()
-    settings = {}
-    settings["forcefield_settings"] = prot_settings.forcefield_settings
-    settings["thermo_settings"] = prot_settings.thermo_settings
-    settings["solvation_settings"] = prot_settings.solvation_settings
-    settings["charge_settings"] = prot_settings.partial_charge_settings
-    settings["integrator_settings"] = prot_settings.integrator_settings
-    settings["output_settings_em"] = prot_settings.output_settings_em
     smc_components = {CN_molecule: off_cn}
     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-        settings, solvent, None, smc_components, tmpdir
+        solvent,
+        None,
+        smc_components,
+        prot_settings.partial_charge_settings,
+        prot_settings.forcefield_settings,
+        prot_settings.integrator_settings,
+        prot_settings.thermo_settings,
+        prot_settings.solvation_settings,
+        prot_settings.output_settings_em,
+        tmpdir,
     )
 
     interchange = create_systems.create_interchange(

From 40ede957f70244c7ff5bf9780ce209a49ae92b4a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 09:07:20 +0000
Subject: [PATCH 23/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../protocols/gromacs_utils/create_systems.py | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_utils/create_systems.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
index ca9d65a..d078d07 100644
--- a/openfe_gromacs/protocols/gromacs_utils/create_systems.py
+++ b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
@@ -45,16 +45,16 @@ def assign_partial_charges(
 
 
 def create_openmm_system(
-        solvent_comp,
-        protein_comp,
-        smc_components,
-        partial_charge_settings,
-        forcefield_settings,
-        integrator_settings,
-        thermo_settings,
-        solvation_settings,
-        output_settings_em,
-        shared_basepath,
+    solvent_comp,
+    protein_comp,
+    smc_components,
+    partial_charge_settings,
+    forcefield_settings,
+    integrator_settings,
+    thermo_settings,
+    solvation_settings,
+    output_settings_em,
+    shared_basepath,
 ):
     """
     Creates the OpenMM system.

From 839130ee1167f8577d9cf5603d01626574a8a540 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 12:18:53 +0200
Subject: [PATCH 24/36] Add tests for residue number and name

---
 .../tests/protocols/test_create_systems.py    | 89 +++++++++++--------
 1 file changed, 53 insertions(+), 36 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index dcf696e..4b06437 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -31,49 +31,66 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
         omm_system, omm_topology, omm_positions, smc_components
     )
     interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
+
     interchange.to_gro(f"{tmpdir}/test.gro")
     gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
+
+    # Testing that the number of atoms is the same
     assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
+    # Testing that atom names are the same
     assert omm_atom_names == interchange_atom_names == gro_atom_names
+    # Testing that residue names are the same
+    interchange_res_names = [atom.metadata["residue_name"] for atom in
+                             interchange.topology.atoms]
+    gro_res_names = GromacsGroFile(f"{tmpdir}/test.gro").residueNames
+    combined_res_names = interchange_res_names + gro_res_names
+    assert len(set(combined_res_names)) == len(set(gro_res_names))
+    # Testing that residue numbers are the same
+    interchange_res_numbers = [atom.metadata["residue_number"] for atom in
+                               interchange.topology.atoms]
+    with open(f"{tmpdir}/test.gro") as f:
+        gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
+    assert interchange_res_numbers == gromacs_res_numbers
+
 
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):
         assert atom_name in interchange_atom_names
 
 
-def test_user_charges(CN_molecule, tmpdir):
-    solvent = gufe.SolventComponent()
-    off_cn = CN_molecule.to_openff()
-    off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
-    off_charges = off_cn.partial_charges
-    prot_settings = GromacsMDProtocol.default_settings()
-    smc_components = {CN_molecule: off_cn}
-    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-        solvent,
-        None,
-        smc_components,
-        prot_settings.partial_charge_settings,
-        prot_settings.forcefield_settings,
-        prot_settings.integrator_settings,
-        prot_settings.thermo_settings,
-        prot_settings.solvation_settings,
-        prot_settings.output_settings_em,
-        tmpdir,
-    )
-
-    interchange = create_systems.create_interchange(
-        omm_system, omm_topology, omm_positions, smc_components
-    )
-    # Save to Gromacs .top file
-    interchange.to_top(f"{tmpdir}/test.top")
-    # Load Gromacs .top file back in as OpenMM system
-    gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
-    # Get the partial charges of the ligand atoms
-    nonbonded = [
-        f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
-    ][0]
-    gro_charges = []
-    for i in range(len(off_charges)):
-        charge, sigma, epsilon = nonbonded.getParticleParameters(i)
-        gro_charges.append(charge._value)
-    np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)
+# def test_user_charges(CN_molecule, tmpdir):
+#     solvent = gufe.SolventComponent()
+#     off_cn = CN_molecule.to_openff()
+#     off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
+#     off_charges = off_cn.partial_charges
+#     prot_settings = GromacsMDProtocol.default_settings()
+#     smc_components = {CN_molecule: off_cn}
+#     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
+#         solvent,
+#         None,
+#         smc_components,
+#         prot_settings.partial_charge_settings,
+#         prot_settings.forcefield_settings,
+#         prot_settings.integrator_settings,
+#         prot_settings.thermo_settings,
+#         prot_settings.solvation_settings,
+#         prot_settings.output_settings_em,
+#         tmpdir,
+#     )
+#
+#     interchange = create_systems.create_interchange(
+#         omm_system, omm_topology, omm_positions, smc_components
+#     )
+#     # Save to Gromacs .top file
+#     interchange.to_top(f"{tmpdir}/test.top")
+#     # Load Gromacs .top file back in as OpenMM system
+#     gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
+#     # Get the partial charges of the ligand atoms
+#     nonbonded = [
+#         f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
+#     ][0]
+#     gro_charges = []
+#     for i in range(len(off_charges)):
+#         charge, sigma, epsilon = nonbonded.getParticleParameters(i)
+#         gro_charges.append(charge._value)
+#     np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)

From f269ff6b1fe8d1fc4a172dacba643f15c5a63edd Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 12:19:18 +0200
Subject: [PATCH 25/36] Add other test back in

---
 .../tests/protocols/test_create_systems.py    | 72 +++++++++----------
 1 file changed, 36 insertions(+), 36 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index 4b06437..9635ba3 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -58,39 +58,39 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
         assert atom_name in interchange_atom_names
 
 
-# def test_user_charges(CN_molecule, tmpdir):
-#     solvent = gufe.SolventComponent()
-#     off_cn = CN_molecule.to_openff()
-#     off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
-#     off_charges = off_cn.partial_charges
-#     prot_settings = GromacsMDProtocol.default_settings()
-#     smc_components = {CN_molecule: off_cn}
-#     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-#         solvent,
-#         None,
-#         smc_components,
-#         prot_settings.partial_charge_settings,
-#         prot_settings.forcefield_settings,
-#         prot_settings.integrator_settings,
-#         prot_settings.thermo_settings,
-#         prot_settings.solvation_settings,
-#         prot_settings.output_settings_em,
-#         tmpdir,
-#     )
-#
-#     interchange = create_systems.create_interchange(
-#         omm_system, omm_topology, omm_positions, smc_components
-#     )
-#     # Save to Gromacs .top file
-#     interchange.to_top(f"{tmpdir}/test.top")
-#     # Load Gromacs .top file back in as OpenMM system
-#     gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
-#     # Get the partial charges of the ligand atoms
-#     nonbonded = [
-#         f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
-#     ][0]
-#     gro_charges = []
-#     for i in range(len(off_charges)):
-#         charge, sigma, epsilon = nonbonded.getParticleParameters(i)
-#         gro_charges.append(charge._value)
-#     np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)
+def test_user_charges(CN_molecule, tmpdir):
+    solvent = gufe.SolventComponent()
+    off_cn = CN_molecule.to_openff()
+    off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
+    off_charges = off_cn.partial_charges
+    prot_settings = GromacsMDProtocol.default_settings()
+    smc_components = {CN_molecule: off_cn}
+    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
+        solvent,
+        None,
+        smc_components,
+        prot_settings.partial_charge_settings,
+        prot_settings.forcefield_settings,
+        prot_settings.integrator_settings,
+        prot_settings.thermo_settings,
+        prot_settings.solvation_settings,
+        prot_settings.output_settings_em,
+        tmpdir,
+    )
+
+    interchange = create_systems.create_interchange(
+        omm_system, omm_topology, omm_positions, smc_components
+    )
+    # Save to Gromacs .top file
+    interchange.to_top(f"{tmpdir}/test.top")
+    # Load Gromacs .top file back in as OpenMM system
+    gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
+    # Get the partial charges of the ligand atoms
+    nonbonded = [
+        f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
+    ][0]
+    gro_charges = []
+    for i in range(len(off_charges)):
+        charge, sigma, epsilon = nonbonded.getParticleParameters(i)
+        gro_charges.append(charge._value)
+    np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)

From 2f80f6ffe6c5ced0264d9053099cea29803189b0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 10:20:02 +0000
Subject: [PATCH 26/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/tests/protocols/test_create_systems.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index 9635ba3..58150d2 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -40,19 +40,20 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     # Testing that atom names are the same
     assert omm_atom_names == interchange_atom_names == gro_atom_names
     # Testing that residue names are the same
-    interchange_res_names = [atom.metadata["residue_name"] for atom in
-                             interchange.topology.atoms]
+    interchange_res_names = [
+        atom.metadata["residue_name"] for atom in interchange.topology.atoms
+    ]
     gro_res_names = GromacsGroFile(f"{tmpdir}/test.gro").residueNames
     combined_res_names = interchange_res_names + gro_res_names
     assert len(set(combined_res_names)) == len(set(gro_res_names))
     # Testing that residue numbers are the same
-    interchange_res_numbers = [atom.metadata["residue_number"] for atom in
-                               interchange.topology.atoms]
+    interchange_res_numbers = [
+        atom.metadata["residue_number"] for atom in interchange.topology.atoms
+    ]
     with open(f"{tmpdir}/test.gro") as f:
         gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
     assert interchange_res_numbers == gromacs_res_numbers
 
-
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):
         assert atom_name in interchange_atom_names

From 031b04b89d20a3aa530e06597961390370063eec Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 14:17:15 +0200
Subject: [PATCH 27/36] Test out new interchange

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 71824fd..a290d07 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,3 +9,4 @@ dependencies:
   - pytest
   - pytest-xdist
   - pytest-cov
+  - openff-interchange>=0.4

From 4e7853084201faefbb20afaaa8bfa12517d970d5 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 14:20:49 +0200
Subject: [PATCH 28/36] Disable residue number check for now till new
 interchange release

---
 environment.yml                                       | 1 -
 openfe_gromacs/tests/protocols/test_create_systems.py | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index a290d07..71824fd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,4 +9,3 @@ dependencies:
   - pytest
   - pytest-xdist
   - pytest-cov
-  - openff-interchange>=0.4
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index 58150d2..90f7a75 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -52,7 +52,7 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     ]
     with open(f"{tmpdir}/test.gro") as f:
         gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
-    assert interchange_res_numbers == gromacs_res_numbers
+#    assert interchange_res_numbers == gromacs_res_numbers
 
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):

From c7dd5038a923a995f9f041c17b935c4c071c3004 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:22:12 +0000
Subject: [PATCH 29/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/tests/protocols/test_create_systems.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index 90f7a75..b57ca5c 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -52,7 +52,7 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     ]
     with open(f"{tmpdir}/test.gro") as f:
         gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
-#    assert interchange_res_numbers == gromacs_res_numbers
+    #    assert interchange_res_numbers == gromacs_res_numbers
 
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):

From e1f996bc420b2386bcc59a3909fbb8dd51ef9e98 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Mon, 30 Sep 2024 14:32:35 +0200
Subject: [PATCH 30/36] Update precommit.yaml

---
 .pre-commit-config.yaml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 342dbda..77221ad 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ ci:
   autoupdate_schedule: "quarterly"
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: check-yaml
   - id: debug-statements
@@ -12,23 +12,28 @@ repos:
   - id: check-executables-have-shebangs
   - id: check-json
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 24.8.0
   hooks:
   - id: black
     files: ^openfe_gromacs
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     files: ^openfe_gromacs
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.1.1
   hooks:
   - id: flake8
     files: ^openfe_gromacs
-    additional_dependencies: [Flake8-pyproject]
+    additional_dependencies: [
+        'flake8-bugbear',
+        'flake8-absolute-import',
+        'flake8-pytest-style==2',
+        'flake8-no-pep420',
+    ]
 - repo: https://github.com/asottile/pyupgrade
-  rev: 'v3.3.1'
+  rev: 'v3.17.0'
   hooks:
   - id: pyupgrade
     args:

From b546e015c0641141edb18b8cc5277120da11e805 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:33:11 +0000
Subject: [PATCH 31/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/protocols/gromacs_md/md_settings.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
index f823b2a..7ab0c78 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_settings.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -146,9 +146,9 @@ class Config:
     """
 
     # # # Bonds # # #
-    constraints: Literal[
-        "none", "h-bonds", "all-bonds", "h-angles", "all-angles"
-    ] = "h-bonds"
+    constraints: Literal["none", "h-bonds", "all-bonds", "h-angles", "all-angles"] = (
+        "h-bonds"
+    )
     """
     Controls which bonds in the topology will be converted to rigid holonomic
     constraints. Note that typical rigid water models do not have bonds, but

From f7ccedff8825dfee3dda44caa1ce81c289e3119f Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:38:36 -0700
Subject: [PATCH 32/36] install openff-interchange from source + re-enable test

---
 environment.yml                                       | 2 ++
 openfe_gromacs/tests/protocols/test_create_systems.py | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 71824fd..a9643c1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,3 +9,5 @@ dependencies:
   - pytest
   - pytest-xdist
   - pytest-cov
+  - pip:
+    - git+https://github.com/openforcefield/openff-interchange.git
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
index b57ca5c..7170bcd 100644
--- a/openfe_gromacs/tests/protocols/test_create_systems.py
+++ b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -52,7 +52,7 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
     ]
     with open(f"{tmpdir}/test.gro") as f:
         gromacs_res_numbers = [int(line[:5].strip()) for line in f.readlines()[2:-1]]
-    #    assert interchange_res_numbers == gromacs_res_numbers
+        assert interchange_res_numbers == gromacs_res_numbers
 
     # check a few atom names to ensure these are not empty sets
     for atom_name in ("HA", "CH3", "CA", "CB"):

From db009fe8657519f241547d2ff9528bac29737b56 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Tue, 1 Oct 2024 09:31:34 +0200
Subject: [PATCH 33/36] Add mdout file to output_settings

---
 .pre-commit-config.yaml                       |   7 +------
 .../protocols/gromacs_md/md_methods.py        |  19 ++++++++++++++++++
 .../protocols/gromacs_md/md_settings.py       |   6 ++++++
 .../protocols/gromacs_utils/write_mdp.py      |   1 +
 .../tests/data/MDProtocol_json_results.gz     | Bin 3622 -> 3704 bytes
 .../data/MDProtocol_json_results_no_EM.gz     | Bin 3564 -> 3633 bytes
 .../tests/protocols/test_gromacs_md.py        |   8 ++++----
 7 files changed, 31 insertions(+), 10 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 77221ad..834451b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -26,12 +26,7 @@ repos:
   hooks:
   - id: flake8
     files: ^openfe_gromacs
-    additional_dependencies: [
-        'flake8-bugbear',
-        'flake8-absolute-import',
-        'flake8-pytest-style==2',
-        'flake8-no-pep420',
-    ]
+    additional_dependencies: [Flake8-pyproject]
 - repo: https://github.com/asottile/pyupgrade
   rev: 'v3.17.0'
   hooks:
diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 046ba9e..5773bed 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -168,6 +168,7 @@ def get_filenames_em(self) -> dict[str, list[pathlib.Path]]:
         - "edr_em"
         - "log_em"
         - "cpt_em"
+        - "grompp_mdp_em"
 
         Returns
         -------
@@ -183,6 +184,7 @@ def get_filenames_em(self) -> dict[str, list[pathlib.Path]]:
             "edr_em",
             "log_em",
             "cpt_em",
+            "grompp_mdp_em",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -231,6 +233,7 @@ def get_filenames_nvt(self) -> dict[str, list[pathlib.Path]]:
         - "edr_nvt"
         - "log_nvt"
         - "cpt_nvt"
+        - "grompp_mdp_nvt"
 
         Returns
         -------
@@ -246,6 +249,7 @@ def get_filenames_nvt(self) -> dict[str, list[pathlib.Path]]:
             "edr_nvt",
             "log_nvt",
             "cpt_nvt",
+            "grompp_mdp_nvt",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -294,6 +298,7 @@ def get_filenames_npt(self) -> dict[str, list[pathlib.Path]]:
         - "edr_npt"
         - "log_npt"
         - "cpt_npt"
+        - "grompp_mdp_npt"
 
         Returns
         -------
@@ -309,6 +314,7 @@ def get_filenames_npt(self) -> dict[str, list[pathlib.Path]]:
             "edr_npt",
             "log_npt",
             "cpt_npt",
+            "grompp_mdp_em",
         ]
         dict_npt = {}
         for file in file_keys:
@@ -403,6 +409,7 @@ def _default_settings(cls):
             engine_settings=GromacsEngineSettings(),
             output_settings_em=EMOutputSettings(
                 mdp_file="em.mdp",
+                grompp_mdp_file="mdout_em.mdp",
                 tpr_file="em.tpr",
                 gro_file="em.gro",
                 trr_file="em.trr",
@@ -413,6 +420,7 @@ def _default_settings(cls):
             ),
             output_settings_nvt=NVTOutputSettings(
                 mdp_file="nvt.mdp",
+                grompp_mdp_file="mdout_nvt.mdp",
                 tpr_file="nvt.tpr",
                 gro_file="nvt.gro",
                 trr_file="nvt.trr",
@@ -423,6 +431,7 @@ def _default_settings(cls):
             ),
             output_settings_npt=NPTOutputSettings(
                 mdp_file="npt.mdp",
+                grompp_mdp_file="mdout_npt.mdp",
                 tpr_file="npt.tpr",
                 gro_file="npt.gro",
                 trr_file="npt.trr",
@@ -735,6 +744,7 @@ def _run_gromacs(
         cpt: str,
         log: str,
         edr: str,
+        out_mdp: str,
         engine_settings: GromacsEngineSettings,
         shared_basebath: pathlib.Path,
     ):
@@ -754,6 +764,7 @@ def _run_gromacs(
         cpt: str
         log: str
         edr: str
+        out_mdp: str
         engine_settings: GromacsEngineSettings
         shared_basebath: Pathlike, optional
           Where to run the calculation, defaults to current working directory
@@ -773,6 +784,8 @@ def _run_gromacs(
                 top,
                 "-o",
                 tpr,
+                "-po",
+                shared_basebath / out_mdp,
             ],
             stdin=subprocess.PIPE,
         )
@@ -894,6 +907,7 @@ def _execute(
                 output_settings_em.cpt_file,
                 output_settings_em.log_file,
                 output_settings_em.edr_file,
+                output_settings_em.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -904,6 +918,7 @@ def _execute(
             output_dict["edr_em"] = shared_basepath / output_settings_em.edr_file
             output_dict["log_em"] = shared_basepath / output_settings_em.log_file
             output_dict["cpt_em"] = shared_basepath / output_settings_em.cpt_file
+            output_dict["grompp_mdp_em"] = shared_basepath / output_settings_em.grompp_mdp_file
 
         # ToDo: Should we disallow running MD without EM?
         # Run NVT
@@ -929,6 +944,7 @@ def _execute(
                 output_settings_nvt.cpt_file,
                 output_settings_nvt.log_file,
                 output_settings_nvt.edr_file,
+                output_settings_nvt.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -939,6 +955,7 @@ def _execute(
             output_dict["edr_nvt"] = shared_basepath / output_settings_nvt.edr_file
             output_dict["log_nvt"] = shared_basepath / output_settings_nvt.log_file
             output_dict["cpt_nvt"] = shared_basepath / output_settings_nvt.cpt_file
+            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
 
         # Run NPT MD simulation
         if sim_settings_npt.nsteps > 0:
@@ -967,6 +984,7 @@ def _execute(
                 output_settings_npt.cpt_file,
                 output_settings_npt.log_file,
                 output_settings_npt.edr_file,
+                output_settings_npt.grompp_mdp_file,
                 engine_settings,
                 ctx.shared,
             )
@@ -977,5 +995,6 @@ def _execute(
             output_dict["edr_npt"] = shared_basepath / output_settings_npt.edr_file
             output_dict["log_npt"] = shared_basepath / output_settings_npt.log_file
             output_dict["cpt_npt"] = shared_basepath / output_settings_npt.cpt_file
+            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
 
         return output_dict
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
index 7ab0c78..d22acdb 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_settings.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -265,6 +265,12 @@ class OutputSettings(SettingsBaseModel):
     Filename for the mdp file for running simulations in Gromacs.
     Default 'em.mdp'
     """
+    grompp_mdp_file: str = "mdout_em.mdp"
+    """
+    Filename for the mdp file that gmx grompp outputs. This file contains 
+    comment lines, as well as the input that gmx grompp has read.
+    Default 'mdout_em.mdp'
+    """
     tpr_file: str = "em.tpr"
     """
     Filename for the tpr file for running simulations in Gromacs.
diff --git a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
index 261b895..eed5b76 100644
--- a/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
+++ b/openfe_gromacs/protocols/gromacs_utils/write_mdp.py
@@ -56,6 +56,7 @@ def dict2mdp(settings_dict: dict, shared_basepath):
     non_mdps = [
         "forcefield_cache",
         "mdp_file",
+        "grompp_mdp_file",
         "tpr_file",
         "trr_file",
         "xtc_file",
diff --git a/openfe_gromacs/tests/data/MDProtocol_json_results.gz b/openfe_gromacs/tests/data/MDProtocol_json_results.gz
index 4355d88f15731754bf37503384d33833afebcd76..1aaae47fd81851fc4c92d3d4a787ce3bdb4e60c2 100644
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diff --git a/openfe_gromacs/tests/protocols/test_gromacs_md.py b/openfe_gromacs/tests/protocols/test_gromacs_md.py
index c5f65cd..533c892 100644
--- a/openfe_gromacs/tests/protocols/test_gromacs_md.py
+++ b/openfe_gromacs/tests/protocols/test_gromacs_md.py
@@ -243,7 +243,7 @@ def test_get_mdp_filenames(self, protocolresult):
     def test_get_filenames_em(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_em()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -264,7 +264,7 @@ def test_get_xtc_em_filename(self, protocolresult):
     def test_get_filenames_nvt(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_nvt()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -285,7 +285,7 @@ def test_get_xtc_nvt_filenames(self, protocolresult):
     def test_get_filenames_npt(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_npt()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, list)
             assert len(file_path) == 1
@@ -323,7 +323,7 @@ def test_reload_protocol_result(self, md_json_no_em):
     def test_get_filenames_em(self, protocolresult):
         dict_file_path = protocolresult.get_filenames_em()
         assert isinstance(dict_file_path, dict)
-        assert len(dict_file_path) == 7
+        assert len(dict_file_path) == 8
         for name, file_path in dict_file_path.items():
             assert isinstance(file_path, type(None))
 

From 33de6fd3ecb9cc377534046fc54d2a7a5cc92506 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 1 Oct 2024 07:32:05 +0000
Subject: [PATCH 34/36] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 openfe_gromacs/protocols/gromacs_md/md_methods.py  | 12 +++++++++---
 openfe_gromacs/protocols/gromacs_md/md_settings.py |  2 +-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 350ed0d..54b9ecd 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -925,7 +925,9 @@ def _execute(
             output_dict["edr_em"] = shared_basepath / output_settings_em.edr_file
             output_dict["log_em"] = shared_basepath / output_settings_em.log_file
             output_dict["cpt_em"] = shared_basepath / output_settings_em.cpt_file
-            output_dict["grompp_mdp_em"] = shared_basepath / output_settings_em.grompp_mdp_file
+            output_dict["grompp_mdp_em"] = (
+                shared_basepath / output_settings_em.grompp_mdp_file
+            )
 
         # ToDo: Should we disallow running MD without EM?
         # Run NVT
@@ -962,7 +964,9 @@ def _execute(
             output_dict["edr_nvt"] = shared_basepath / output_settings_nvt.edr_file
             output_dict["log_nvt"] = shared_basepath / output_settings_nvt.log_file
             output_dict["cpt_nvt"] = shared_basepath / output_settings_nvt.cpt_file
-            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
+            output_dict["grompp_mdp_nvt"] = (
+                shared_basepath / output_settings_nvt.grompp_mdp_file
+            )
 
         # Run NPT MD simulation
         if sim_settings_npt.nsteps > 0:
@@ -1002,6 +1006,8 @@ def _execute(
             output_dict["edr_npt"] = shared_basepath / output_settings_npt.edr_file
             output_dict["log_npt"] = shared_basepath / output_settings_npt.log_file
             output_dict["cpt_npt"] = shared_basepath / output_settings_npt.cpt_file
-            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
+            output_dict["grompp_mdp_nvt"] = (
+                shared_basepath / output_settings_nvt.grompp_mdp_file
+            )
 
         return output_dict
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
index d22acdb..f6a5e0b 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_settings.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -267,7 +267,7 @@ class OutputSettings(SettingsBaseModel):
     """
     grompp_mdp_file: str = "mdout_em.mdp"
     """
-    Filename for the mdp file that gmx grompp outputs. This file contains 
+    Filename for the mdp file that gmx grompp outputs. This file contains
     comment lines, as well as the input that gmx grompp has read.
     Default 'mdout_em.mdp'
     """

From c84ea909065f51fb5051fe4bbaf86d4e8719d34c Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Tue, 1 Oct 2024 09:38:00 +0200
Subject: [PATCH 35/36] Remove unused imports

---
 openfe_gromacs/protocols/gromacs_md/md_methods.py    | 12 +++---------
 .../protocols/gromacs_utils/create_systems.py        |  8 +-------
 openfe_gromacs/tests/conftest.py                     |  1 -
 .../tests/protocols/test_md_tokenization.py          |  1 -
 4 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
index 350ed0d..e1efeb8 100644
--- a/openfe_gromacs/protocols/gromacs_md/md_methods.py
+++ b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -20,15 +20,9 @@
 from typing import Any
 
 import gufe
-import pint
-from gufe import ChemicalSystem, SmallMoleculeComponent, settings
-from openfe.protocols.openmm_utils import (
-    charge_generation,
-    system_creation,
-    system_validation,
-)
-from openfe.utils import log_system_probe, without_oechem_backend
-from openff.interchange import Interchange
+from gufe import ChemicalSystem, settings
+from openfe.protocols.openmm_utils import system_validation
+from openfe.utils import log_system_probe
 from openff.toolkit.topology import Molecule as OFFMolecule
 from openff.units import unit
 
diff --git a/openfe_gromacs/protocols/gromacs_utils/create_systems.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
index d078d07..3c38db5 100644
--- a/openfe_gromacs/protocols/gromacs_utils/create_systems.py
+++ b/openfe_gromacs/protocols/gromacs_utils/create_systems.py
@@ -9,13 +9,7 @@
 from openff.units.openmm import from_openmm, to_openmm
 from openmmtools import forces
 
-from openfe_gromacs.protocols.gromacs_md.md_settings import (
-    EMOutputSettings,
-    FFSettingsOpenMM,
-    IntegratorSettings,
-    OpenFFPartialChargeSettings,
-    SolvationSettings,
-)
+from openfe_gromacs.protocols.gromacs_md.md_settings import OpenFFPartialChargeSettings
 
 
 def assign_partial_charges(
diff --git a/openfe_gromacs/tests/conftest.py b/openfe_gromacs/tests/conftest.py
index 62fa118..eec6ab7 100644
--- a/openfe_gromacs/tests/conftest.py
+++ b/openfe_gromacs/tests/conftest.py
@@ -2,7 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import importlib
 import os
-import pathlib
 from importlib import resources
 
 import gufe
diff --git a/openfe_gromacs/tests/protocols/test_md_tokenization.py b/openfe_gromacs/tests/protocols/test_md_tokenization.py
index 90836d4..6a510a1 100644
--- a/openfe_gromacs/tests/protocols/test_md_tokenization.py
+++ b/openfe_gromacs/tests/protocols/test_md_tokenization.py
@@ -3,7 +3,6 @@
 import json
 
 import gufe
-import openfe
 import pytest
 from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
 

From 9ec736cac3a4a938e9f29a1942d2bcf29aa78ece Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Tue, 1 Oct 2024 09:48:14 +0200
Subject: [PATCH 36/36] Update token

---
 openfe_gromacs/tests/protocols/test_md_tokenization.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openfe_gromacs/tests/protocols/test_md_tokenization.py b/openfe_gromacs/tests/protocols/test_md_tokenization.py
index 6a510a1..4969494 100644
--- a/openfe_gromacs/tests/protocols/test_md_tokenization.py
+++ b/openfe_gromacs/tests/protocols/test_md_tokenization.py
@@ -40,7 +40,7 @@ def protocol_result(md_json):
 
 class TestGromacsMDProtocol(GufeTokenizableTestsMixin):
     cls = gromacs_md.GromacsMDProtocol
-    key = "GromacsMDProtocol-c75de773fddf547f15daf4c01a455c66"
+    key = "GromacsMDProtocol-829ed8e2ddfff11f9e86eec044222317"
     repr = f"<{key}>"
 
     @pytest.fixture()