From c59456a4fc78b55f9763c2d6cc7a2afdefe0c82f Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 9 Apr 2026 22:43:29 -0400
Subject: [PATCH 01/18] Using gufe mapping charge difference utility

---
 feflow/protocols/nonequilibrium_cycling.py | 13 ++-----------
 feflow/utils/charge.py                     |  4 ----
 2 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index 1fe639ff..46980e35 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -239,17 +239,8 @@ def _execute(self, ctx, *, protocol, state_a, state_b, mapping, **inputs):
         )
 
         # Handle charge corrections/transformations
-        # Get the change difference between the end states
-        # and check if the charge correction used is appropriate
-        try:  # Catch unsupported charges differences and raise protocol error
-            charge_difference = get_alchemical_charge_difference(
-                mapping,
-                forcefield_settings.nonbonded_method,
-                alchemical_settings.explicit_charge_correction,
-                solvent_comp_a,  # Solvent comp in a is expected to be the same as in b
-            )
-        except ValueError as e:
-            raise ProtocolSupportError(str(e))
+        # Get the formal change difference between the end states
+        charge_difference = mapping.get_alchemical_charge_difference()
 
         if alchemical_settings.explicit_charge_correction:
             alchem_water_resids = _rfe_utils.topologyhelpers.get_alchemical_waters(
diff --git a/feflow/utils/charge.py b/feflow/utils/charge.py
index 143a55a9..b21c156e 100644
--- a/feflow/utils/charge.py
+++ b/feflow/utils/charge.py
@@ -7,10 +7,6 @@
 from openfe.protocols.openmm_utils.charge_generation import (
     assign_offmol_partial_charges,
 )
-from openfe.protocols.openmm_rfe.equil_rfe_methods import (
-    _get_alchemical_charge_difference,
-)
 
 # TODO: Importing from OpenFE for now, should we migrate them here?
 assign_offmol_partial_charges = assign_offmol_partial_charges
-get_alchemical_charge_difference = _get_alchemical_charge_difference

From 28a666226bce3d47fc511a24a5948ac987058e80 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 9 Apr 2026 22:44:04 -0400
Subject: [PATCH 02/18] Using 1.9 gufe/openfe releases

---
 devtools/conda-envs/test_env.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index a9c0a2ef..921a9ad0 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -4,9 +4,9 @@ channels:
   - openeye
 dependencies:
     # Base depends
-  - gufe ~=1.7.1
+  - gufe ~=1.9.0
   - numpy
-  - openfe ~=1.8.0   # TODO: Remove once we don't depend on openfe
+  - openfe ~=1.9.0   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From e07522d3f1b39c3fd060b3a517b5aaa33b440cb1 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 9 Apr 2026 22:51:15 -0400
Subject: [PATCH 03/18] gufe 1.9 support requires openfe 1.10

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 1293e885..1c729955 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe ~=1.9.0
   - numpy
-  - openfe ~=1.9.0   # TODO: Remove once we don't depend on openfe
+  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From 054ab37b7bfdf75c10b91edae2c3d03c17e67508 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 9 Apr 2026 23:00:16 -0400
Subject: [PATCH 04/18] Removing now unexisting import

---
 feflow/protocols/nonequilibrium_cycling.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index 46980e35..5b463690 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -113,7 +113,6 @@ def _execute(self, ctx, *, protocol, state_a, state_b, mapping, **inputs):
             get_alchemical_components,
         )
         from feflow.utils.hybrid_topology import HybridTopologyFactory
-        from feflow.utils.charge import get_alchemical_charge_difference
         from feflow.utils.misc import register_ff_parameters_template
 
         # Get receptor components from systems if found (None otherwise)

From 8da0403f2deefdcc30cda8b5396af9942124f988 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:17:12 -0400
Subject: [PATCH 05/18] Use CPU platform for tests

---
 feflow/tests/test_protein_mutation.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/feflow/tests/test_protein_mutation.py b/feflow/tests/test_protein_mutation.py
index 4c151eb0..0ac8aec2 100644
--- a/feflow/tests/test_protein_mutation.py
+++ b/feflow/tests/test_protein_mutation.py
@@ -636,6 +636,8 @@ def test_double_charge_fails(
         from feflow.utils.exceptions import ProtocolSupportError
 
         settings = NonEquilibriumCyclingProtocol.default_settings()
+        # Change engine platform for tests
+        settings.engine_settings.compute_platform = "CPU"
         # We need to make sure we enable the alchemical charge correction
         settings.alchemical_settings.explicit_charge_correction = True
 

From fc94b80ecd568dd1c8abd44521b233a5a3bb372d Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:22:32 -0400
Subject: [PATCH 06/18] gufe support following semver

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 1c729955..0586ccc8 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -4,7 +4,7 @@ channels:
   - openeye
 dependencies:
     # Base depends
-  - gufe ~=1.9.0
+  - gufe >=1.9.0,<2
   - numpy
   - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
   - openff-units

From 0401ad3ab7e0be55d3fa2df2704a2a17fa58d9b2 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:23:21 -0400
Subject: [PATCH 07/18] openfe support following semver

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 0586ccc8..4c8a3a95 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe >=1.9.0,<2
   - numpy
-  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
+  - openfe >=1.10.0,<2   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From 75d8ddab7894799214deb5a9f30a50318848a85c Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:41:55 -0400
Subject: [PATCH 08/18] openfe >=1.11 does not support neq integrators

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 4c8a3a95..0586ccc8 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe >=1.9.0,<2
   - numpy
-  - openfe >=1.10.0,<2   # TODO: Remove once we don't depend on openfe
+  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From f29c7f821777132caf13ef9121c5b6e7b9b39cca Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 13:46:45 -0400
Subject: [PATCH 09/18] removing unused barostat setting

---
 feflow/settings/integrators.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index 48d7a9f4..695457e7 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -35,12 +35,6 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
-    barostat_frequency: TimestepQuantity = 25 * unit.timestep
-    """
-    Frequency at which volume scaling changes should be attempted.
-    Note: The barostat frequency is ignored for gas-phase simulations.
-    Default 25 * unit.timestep.
-    """
     remove_com: bool = False
     """
     Whether or not to remove the center of mass motion. Default False.

From cda67bd412b74fc5f69b3e731fd882e61a9cca94 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 14:00:03 -0400
Subject: [PATCH 10/18] Revert "removing unused barostat setting"

This reverts commit f29c7f821777132caf13ef9121c5b6e7b9b39cca.
---
 feflow/settings/integrators.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index 695457e7..48d7a9f4 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -35,6 +35,12 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
+    barostat_frequency: TimestepQuantity = 25 * unit.timestep
+    """
+    Frequency at which volume scaling changes should be attempted.
+    Note: The barostat frequency is ignored for gas-phase simulations.
+    Default 25 * unit.timestep.
+    """
     remove_com: bool = False
     """
     Whether or not to remove the center of mass motion. Default False.

From 36963323fbc62f9537a93aa545d0c753011a32c5 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Tue, 9 Jun 2026 14:44:34 -0400
Subject: [PATCH 11/18] Adding barostat attribute to support openfe 1.11+

---
 devtools/conda-envs/test_env.yaml | 2 +-
 feflow/settings/integrators.py    | 9 ++++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 0586ccc8..4c8a3a95 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe >=1.9.0,<2
   - numpy
-  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
+  - openfe >=1.10.0,<2   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this
diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index 48d7a9f4..dbf79e68 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -6,7 +6,7 @@
 for the specific integrator settings.
 """
 
-from typing import Annotated, TypeAlias
+from typing import Annotated, TypeAlias, Literal
 
 from pydantic import ConfigDict, field_validator
 
@@ -35,6 +35,13 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
+    barostat: Literal["MonteCarloBarostat", "MonteCarloMembraneBarostat"] = "MonteCarloBarostat"
+    """
+    The barostat to be used in the simulations. Default MonteCarloBarostat.
+    Notes
+    -----
+    If the system contains a membrane, use the `MonteCarloMembraneBarostat`.
+    """
     barostat_frequency: TimestepQuantity = 25 * unit.timestep
     """
     Frequency at which volume scaling changes should be attempted.

From 2d43609563f04b4699b4058a0dbd56dceee905bb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 9 Jun 2026 18:46:22 +0000
Subject: [PATCH 12/18] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 feflow/settings/integrators.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index dbf79e68..00590c53 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -35,7 +35,9 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
-    barostat: Literal["MonteCarloBarostat", "MonteCarloMembraneBarostat"] = "MonteCarloBarostat"
+    barostat: Literal["MonteCarloBarostat", "MonteCarloMembraneBarostat"] = (
+        "MonteCarloBarostat"
+    )
     """
     The barostat to be used in the simulations. Default MonteCarloBarostat.
     Notes

From 1ebb346b3ee293b4cd08d482514d56c0ee85d636 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Wed, 10 Jun 2026 11:05:10 -0400
Subject: [PATCH 13/18] testing CI with openfe 1.10.x

---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 4c8a3a95..0586ccc8 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe >=1.9.0,<2
   - numpy
-  - openfe >=1.10.0,<2   # TODO: Remove once we don't depend on openfe
+  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From 49c3283eb1cd60d968846ecbfbb38a67a5b2c0c0 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 11 Jun 2026 18:09:58 -0400
Subject: [PATCH 14/18] Validating charge changing transformations

---
 feflow/protocols/nonequilibrium_cycling.py | 12 ++-
 feflow/utils/charge.py                     | 97 +++++++++++++++++++++-
 2 files changed, 107 insertions(+), 2 deletions(-)

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index 5b463690..9e0c5628 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -30,6 +30,7 @@
 from openff.units.openmm import to_openmm, from_openmm
 
 from ..settings import NonEquilibriumCyclingSettings
+from ..utils.charge import validate_charge_difference
 from ..utils.data import serialize, deserialize
 from ..utils.exceptions import ProtocolSupportError
 from ..utils.misc import (
@@ -239,7 +240,16 @@ def _execute(self, ctx, *, protocol, state_a, state_b, mapping, **inputs):
 
         # Handle charge corrections/transformations
         # Get the formal change difference between the end states
-        charge_difference = mapping.get_alchemical_charge_difference()
+        try:
+            charge_difference = validate_charge_difference(
+                mapping,
+                forcefield_settings.nonbonded_method,
+                alchemical_settings.explicit_charge_correction,
+                solvent_comp_a,  # Solvent comp in a is expected to be the same as in b
+            )
+        except ValueError as e:
+            raise ProtocolSupportError(str(e))
+
 
         if alchemical_settings.explicit_charge_correction:
             alchem_water_resids = _rfe_utils.topologyhelpers.get_alchemical_waters(
diff --git a/feflow/utils/charge.py b/feflow/utils/charge.py
index b21c156e..391f10e4 100644
--- a/feflow/utils/charge.py
+++ b/feflow/utils/charge.py
@@ -3,10 +3,105 @@
 Such as assigning both formal and partial charges, or transforming solvent into ions
 or vice versa for charge-changing alchemical transformations.
 """
-
+import logging
+import warnings
+from gufe import LigandAtomMapping, SolventComponent
 from openfe.protocols.openmm_utils.charge_generation import (
     assign_offmol_partial_charges,
 )
 
 # TODO: Importing from OpenFE for now, should we migrate them here?
 assign_offmol_partial_charges = assign_offmol_partial_charges
+
+logger = logging.getLogger(__name__)
+
+
+# TODO: Re-evaluate if we want a more global utility function for this in the openfe "ecosystem"
+# Vendored from openfe protocol method in https://github.com/OpenFreeEnergy/openfe/blob/75cb2e85a46514633ecfe33353dfa5e9dc22e729/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py#L373
+def validate_charge_difference(
+        mapping: LigandAtomMapping,
+        nonbonded_method: str,
+        explicit_charge_correction: bool,
+        solvent_component: SolventComponent | None,
+) -> int:
+    """
+    Validates the net charge difference between the two states.
+
+    Useful for uses in Hybrid Topology protocols where alchemical changes
+    of 2 or more charge units are not supported, and/or not using PME
+    when there is charge correction is not supported.
+
+    Parameters
+    ----------
+    mapping : LigandAtomMapping
+      Mapping object between transforming components.
+    nonbonded_method : str
+      The OpenMM nonbonded method used for the simulation.
+    explicit_charge_correction : bool
+      Whether to use an explicit charge correction.
+    solvent_component : openfe.SolventComponent | None
+      The SolventComponent of the simulation.
+
+    Returns
+    -------
+    int
+      The alchemical charge difference between the two states.
+
+    Raises
+    ------
+    ValueError
+      * If an explicit charge correction is attempted and the
+        nonbonded method is not PME.
+      * If the absolute charge difference is greater than one
+        and an explicit charge correction is attempted.
+      * If an explicit charge correction is attempted and there is no
+        solvent present.
+    UserWarning
+      * If there is any charge difference and no explicit charge
+        correction has been requested.
+    """
+    difference = mapping.get_alchemical_charge_difference()
+
+    if abs(difference) == 0:
+        return difference
+
+    if not explicit_charge_correction:
+        wmsg = (
+            f"A charge difference of {difference} is observed "
+            "between the end states. No charge correction has "
+            "been requested, please account for this in your "
+            "final results."
+        )
+        logger.warning(wmsg)
+        warnings.warn(wmsg)
+        return difference
+
+    if solvent_component is None:
+        errmsg = "Cannot use explicit charge correction without solvent"
+        raise ValueError(errmsg)
+
+    # We implicitly check earlier that we have to have pme for a solvated
+    # system, so we only need to check the nonbonded method here
+    if nonbonded_method.lower() != "pme":
+        errmsg = "Explicit charge correction when not using PME is not currently supported."
+        raise ValueError(errmsg)
+
+    if abs(difference) > 1:
+        errmsg = (
+            f"A charge difference of {difference} is observed "
+            "between the end states and an explicit charge  "
+            "correction has been requested. Unfortunately "
+            "only absolute differences of 1 are supported."
+        )
+        raise ValueError(errmsg)
+
+    ion = {-1: solvent_component.positive_ion, 1: solvent_component.negative_ion}[difference]
+
+    wmsg = (
+        f"A charge difference of {difference} is observed "
+        "between the end states. This will be addressed by "
+        f"transforming a water into a {ion} ion"
+    )
+    logger.info(wmsg)
+
+    return difference

From f48ba0c888eeb4574b7e1e4d970eb96200780f0b Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 11 Jun 2026 18:16:18 -0400
Subject: [PATCH 15/18] Test executing unit only. Avoiding whole DAG execution.

---
 feflow/tests/test_protein_mutation.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/feflow/tests/test_protein_mutation.py b/feflow/tests/test_protein_mutation.py
index 0ac8aec2..e16d9fee 100644
--- a/feflow/tests/test_protein_mutation.py
+++ b/feflow/tests/test_protein_mutation.py
@@ -617,12 +617,12 @@ def test_double_charge_fails(
     ):
         """
         Test that attempting a mutation with a double charge change between lysine and glutamate
-        systems raises a `NotSupportedError`.
+        systems raises a `ProtocolSupportError`.
 
         This test verifies that the `NonEquilibriumCyclingProtocol` correctly raises an error when trying to
-        create a directed acyclic graph (DAG) for an invalid mutation involving a double charge change.
-        The test expects the `NotSupportedError` to be raised with a message indicating that
-        double-charge transformations are not supported.
+        execute the setup of an invalid mutation involving a double charge change. The charge
+        validation happens in the `SetupUnit`, so we only execute that unit directly instead of
+        running the full DAG (which would also run the, much more expensive, simulation units).
 
         Parameters
         ----------
@@ -633,6 +633,7 @@ def test_double_charge_fails(
         lys_to_glu_mapping : LigandAtomMapping
             Atom mapping defining the correspondence between atoms in the lysine and glutamate systems.
         """
+        from gufe.protocols.protocolunit import Context
         from feflow.utils.exceptions import ProtocolSupportError
 
         settings = NonEquilibriumCyclingProtocol.default_settings()
@@ -646,11 +647,14 @@ def test_double_charge_fails(
         dag = protocol.create(
             stateA=lys_capped_system,
             stateB=glu_capped_system,
-            name="Invalid proline mutation",
+            name="Invalid double charge mutation",
             mapping=lys_to_glu_mapping,
         )
 
-        # Expect an error when trying to create the DAG with this invalid transformation
+        # Charge validation happens in the setup unit -- run only that unit
+        setup_unit = dag.protocol_units[0]
+
+        # Expect an error when trying to execute the setup for this invalid transformation
         with pytest.raises(ProtocolSupportError):
             with tmpdir.as_cwd():
                 shared = Path("shared")
@@ -659,4 +663,7 @@ def test_double_charge_fails(
                 scratch = Path("scratch")
                 scratch.mkdir()
 
-                execute_DAG(dag, shared_basedir=shared, scratch_basedir=scratch)
+                context = Context(shared=shared, scratch=scratch)
+                setup_unit.execute(
+                    context=context, raise_error=True, **setup_unit.inputs
+                )

From 403ace19ad08b0d16b4538a33b46156160911dca Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 11 Jun 2026 18:20:31 -0400
Subject: [PATCH 16/18] Revert "testing CI with openfe 1.10.x"

This reverts commit 1ebb346b3ee293b4cd08d482514d56c0ee85d636.
---
 devtools/conda-envs/test_env.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index 0586ccc8..4c8a3a95 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -6,7 +6,7 @@ dependencies:
     # Base depends
   - gufe >=1.9.0,<2
   - numpy
-  - openfe ~=1.10.0   # TODO: Remove once we don't depend on openfe
+  - openfe >=1.10.0,<2   # TODO: Remove once we don't depend on openfe
   - openff-units
   - openmm
   - openmmforcefields >=0.14.1  # TODO: remove when upstream deps fix this

From 2d838fbf756d901de42524818bade15ce289ff49 Mon Sep 17 00:00:00 2001
From: ijpulidos <2949729+ijpulidos@users.noreply.github.com>
Date: Thu, 11 Jun 2026 18:21:43 -0400
Subject: [PATCH 17/18] We only support MonteCarloBarostat for now

---
 feflow/settings/integrators.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index 00590c53..81844ecc 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -35,7 +35,7 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
-    barostat: Literal["MonteCarloBarostat", "MonteCarloMembraneBarostat"] = (
+    barostat: Literal["MonteCarloBarostat"] = (
         "MonteCarloBarostat"
     )
     """

From 2d2d7f9b592e81eeeb4625e6b099a37ee066f746 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 11 Jun 2026 22:24:12 +0000
Subject: [PATCH 18/18] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 feflow/protocols/nonequilibrium_cycling.py |  1 -
 feflow/settings/integrators.py             |  4 +---
 feflow/utils/charge.py                     | 17 +++++++++++------
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index 9e0c5628..edf1358a 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -250,7 +250,6 @@ def _execute(self, ctx, *, protocol, state_a, state_b, mapping, **inputs):
         except ValueError as e:
             raise ProtocolSupportError(str(e))
 
-
         if alchemical_settings.explicit_charge_correction:
             alchem_water_resids = _rfe_utils.topologyhelpers.get_alchemical_waters(
                 state_a_topology,
diff --git a/feflow/settings/integrators.py b/feflow/settings/integrators.py
index 81844ecc..26a0dc45 100644
--- a/feflow/settings/integrators.py
+++ b/feflow/settings/integrators.py
@@ -35,9 +35,7 @@ class PeriodicNonequilibriumIntegratorSettings(SettingsBaseModel):
     """Number of steps for the equilibrium parts of the cycle. Default 12500"""
     nonequilibrium_steps: int = 12500
     """Number of steps for the non-equilibrium parts of the cycle. Default 12500"""
-    barostat: Literal["MonteCarloBarostat"] = (
-        "MonteCarloBarostat"
-    )
+    barostat: Literal["MonteCarloBarostat"] = "MonteCarloBarostat"
     """
     The barostat to be used in the simulations. Default MonteCarloBarostat.
     Notes
diff --git a/feflow/utils/charge.py b/feflow/utils/charge.py
index 391f10e4..ef102e8d 100644
--- a/feflow/utils/charge.py
+++ b/feflow/utils/charge.py
@@ -3,6 +3,7 @@
 Such as assigning both formal and partial charges, or transforming solvent into ions
 or vice versa for charge-changing alchemical transformations.
 """
+
 import logging
 import warnings
 from gufe import LigandAtomMapping, SolventComponent
@@ -19,10 +20,10 @@
 # TODO: Re-evaluate if we want a more global utility function for this in the openfe "ecosystem"
 # Vendored from openfe protocol method in https://github.com/OpenFreeEnergy/openfe/blob/75cb2e85a46514633ecfe33353dfa5e9dc22e729/src/openfe/protocols/openmm_rfe/hybridtop_protocols.py#L373
 def validate_charge_difference(
-        mapping: LigandAtomMapping,
-        nonbonded_method: str,
-        explicit_charge_correction: bool,
-        solvent_component: SolventComponent | None,
+    mapping: LigandAtomMapping,
+    nonbonded_method: str,
+    explicit_charge_correction: bool,
+    solvent_component: SolventComponent | None,
 ) -> int:
     """
     Validates the net charge difference between the two states.
@@ -83,7 +84,9 @@ def validate_charge_difference(
     # We implicitly check earlier that we have to have pme for a solvated
     # system, so we only need to check the nonbonded method here
     if nonbonded_method.lower() != "pme":
-        errmsg = "Explicit charge correction when not using PME is not currently supported."
+        errmsg = (
+            "Explicit charge correction when not using PME is not currently supported."
+        )
         raise ValueError(errmsg)
 
     if abs(difference) > 1:
@@ -95,7 +98,9 @@ def validate_charge_difference(
         )
         raise ValueError(errmsg)
 
-    ion = {-1: solvent_component.positive_ion, 1: solvent_component.negative_ion}[difference]
+    ion = {-1: solvent_component.positive_ion, 1: solvent_component.negative_ion}[
+        difference
+    ]
 
     wmsg = (
         f"A charge difference of {difference} is observed "