diff --git a/dimsim/compute/apps.py b/dimsim/compute/apps.py
index 47d5937..6ffb428 100644
--- a/dimsim/compute/apps.py
+++ b/dimsim/compute/apps.py
@@ -1,8 +1,12 @@
 import openmm
+import openmm.app
 from openff.toolkit import Topology
+from parsl import File
 from parsl.app.app import python_app
 
 from dimsim.configs.compute.density import DensityConfig
+from dimsim.configs.compute.equilibration import EquilibrationConfig
+from dimsim.configs.compute.minimization import MinimizationConfig, default_minimization_config
 
 
 @python_app
@@ -104,30 +108,28 @@ def prepare_openmm_system(
 
 
 @python_app
-def minimize_energy(
-    system_future: dict[str, DensityConfig | openmm.System], job_dir: str
-) -> dict[str, DensityConfig | float]:
+def prepare_openmm_simulation(
+    system_future: dict[str, DensityConfig | openmm.System],
+    job_dir: str,
+) -> dict[str, DensityConfig | tuple[File, File, File, File]]:
     import logging
 
-    import openmm
-    import openmm.app
-    import openmm.unit
     from openff.toolkit import Molecule, Topology
 
     logging.basicConfig(
         filename=f"{job_dir}/simulation.log",
         level=logging.INFO,
     )
-    logging.info("Starting energy minimization app")
+    logging.info("Starting OpenMM simulation creation app")
     system = system_future["openmm_system"]
 
-    data_entry = system_future["compute_config"]["target"]
+    compute_config: DensityConfig = system_future["compute_config"]
+    data_entry = compute_config["target"]
 
     # this should be in Kelvin
-    temperature = system_future["compute_config"]["target"]["temperature"]
+    temperature = compute_config["target"]["temperature"]
 
     packed_topology_file = f"{job_dir}/packed_topology.pdb"
-    minimized_topology_file = f"{job_dir}/minimized_topology.pdb"
 
     molecules = [Molecule.from_smiles(smiles) for smiles in data_entry["smiles"]]
 
@@ -142,20 +144,75 @@ def minimize_energy(
         integrator=openmm.LangevinMiddleIntegrator(
             temperature * openmm.unit.kelvin,
             1.0 / openmm.unit.picosecond,
-            1.0 * openmm.unit.femtoseconds,
+            1.0 * openmm.unit.femtoseconds,  # TODO: This should be wired to user-valuable
         ),
     )
 
     simulation.context.setPositions(topology.get_positions().to_openmm())
 
-    original_state = simulation.context.getState(energy=True)
+    simulation_files = [
+        File(f"{job_dir}/simulation_toology.pdb"),
+        File(f"{job_dir}/simulation_system.xml"),
+        File(f"{job_dir}/simulation_integrator.xml"),
+        File(f"{job_dir}/simulation_checkpoint.chk"),
+    ]
+
+    with open(simulation_files[0].filepath, "w") as f:
+        openmm.app.PDBFile.writeFile(
+            topology=simulation.topology,
+            positions=simulation.context.getState(getPositions=True).getPositions(),
+            file=f,
+        )
+
+    with open(simulation_files[1].filepath, "w") as f:
+        f.write(openmm.XmlSerializer.serialize(simulation.system))
+
+    with open(simulation_files[2].filepath, "w") as f:
+        f.write(openmm.XmlSerializer.serialize(simulation.integrator))
+
+    simulation.saveCheckpoint(simulation_files[3].filepath)
+
+    return {
+        "compute_config": compute_config,
+        "simulation_files": tuple(simulation_files),
+    }
+
+
+@python_app
+def minimize_energy(
+    simulation_future: dict[str, DensityConfig | tuple[File, File, File, File]],
+    job_dir: str,
+    minimization_config: MinimizationConfig = default_minimization_config,
+) -> dict[str, DensityConfig | float | tuple[File]]:
+    import logging
+
+    import openmm
+    import openmm.app
+    import openmm.unit
+
+    minimized_topology_file = f"{job_dir}/minimized_topology.pdb"
+
+    simulation_files: tuple[File, File, File, File] = simulation_future["simulation_files"]
 
-    simulation.minimizeEnergy()
+    with open(simulation_files[0].filepath) as f:
+        topology = openmm.app.PDBFile(f).getTopology()
 
-    # simulation.reporters.append(openmm.app.DCDReporter(outputs[0].filepath, 100))
+    with open(simulation_files[1].filepath) as f:
+        system = openmm.XmlSerializer.deserialize(f.read())
 
-    # print("Minimized energy, now running 10,000 steps of dynamics...")
-    # simulation.step(10_000)
+    with open(simulation_files[2].filepath) as f:
+        integrator = openmm.XmlSerializer.deserialize(f.read())
+
+    with open(simulation_files[3].filepath, "rb") as f:
+        simulation = openmm.app.Simulation(topology, system, integrator)
+        simulation.loadCheckpoint(f)
+
+    original_state = simulation.context.getState(energy=True)
+
+    simulation.minimizeEnergy(
+        tolerance=minimization_config["tolerance"],
+        maxIterations=minimization_config["max_iterations"],
+    )
 
     final_state = simulation.context.getState(energy=True, positions=True)
 
@@ -167,7 +224,92 @@ def minimize_energy(
 
     logging.info(f"Minimized energy from {original:.2f} to {final:.2f}")
 
-    return original, final
+    minimized_files: list[File] = [
+        File(f"{job_dir}/minimized_topology.pdb"),
+        File(f"{job_dir}/minimized_system.xml"),
+        File(f"{job_dir}/minimized_integrator.xml"),
+        File(f"{job_dir}/minimized_checkpoint.chk"),
+    ]
+
+    with open(minimized_files[0].filepath, "w") as f:
+        openmm.app.PDBFile.writeFile(
+            topology=simulation.topology,
+            positions=simulation.context.getState(getPositions=True).getPositions(),
+            file=f,
+        )
+
+    with open(minimized_files[1].filepath, "w") as f:
+        f.write(openmm.XmlSerializer.serialize(simulation.system))
+
+    with open(minimized_files[2].filepath, "w") as f:
+        f.write(openmm.XmlSerializer.serialize(simulation.integrator))
+
+    simulation.saveCheckpoint(minimized_files[3].filepath)
+
+    return {
+        "compute_config": simulation_future["compute_config"],
+        "original_energy": original,
+        "final_energy": final,
+        "simulation_files": tuple(minimized_files),
+    }
+
+
+@python_app
+def run_equilibration(
+    compute_config: DensityConfig,
+    equilibration_config: EquilibrationConfig,
+    minimization_future: dict[str, DensityConfig | float | tuple[File]],
+    job_dir: str,
+) -> dict[str, File]:
+    # TODO: Expose barostat (+ thermostat?) to user
+
+    minimized_files: tuple[File, File, File, File] = minimization_future["simulation_files"]
+
+    with open(minimized_files[0].filepath) as f:
+        topology = openmm.app.PDBFile(f).getTopology()
+
+    with open(minimized_files[1].filepath) as f:
+        system = openmm.XmlSerializer.deserialize(f.read())
+
+    with open(minimized_files[2].filepath) as f:
+        integrator = openmm.XmlSerializer.deserialize(f.read())
+
+    with open(minimized_files[3].filepath, "rb") as f:
+        simulation = openmm.app.Simulation(topology, system, integrator)
+        simulation.loadCheckpoint(f)
+
+    simulation.system.addForce(
+        openmm.MonteCarloBarostat(
+            1.0 * openmm.unit.atmosphere,
+            300.0 * openmm.unit.kelvin,
+        )
+    )
+
+    simulation.context.reinitialize(preserveState=True)
+
+    trajectory_file = File(f"{job_dir}/trajectory.dcd")
+    data_file = File(f"{job_dir}/simulation_data.log")
+
+    simulation.reporters.append(
+        openmm.app.StateDataReporter(
+            file=data_file.filepath,
+            reportInterval=1000,
+            step=True,
+            potentialEnergy=True,
+            kineticEnergy=True,
+            totalEnergy=True,
+            temperature=True,
+            volume=True,
+            density=True,
+            speed=True,
+        )
+    )
+
+    simulation.reporters.append(openmm.app.DCDReporter(trajectory_file.filepath, 1000))
+
+    simulation.step(equilibration_config["steps_per_iteration"])
+
+    return {"trajectory_file": trajectory_file}
 
 
 @python_app
diff --git a/dimsim/compute/equilibration.py b/dimsim/compute/equilibration.py
new file mode 100644
index 0000000..c1fd649
--- /dev/null
+++ b/dimsim/compute/equilibration.py
@@ -0,0 +1,13 @@
+import numpy
+import polars
+import red
+
+
+def assert_equilibrated(simulation_data: polars.DataFrame) -> bool:
+    idx, _g, ess = red.detect_equilibration_window(
+        numpy.array(simulation_data["Potential Energy (kJ/mole)"]),
+        method="min_sse",
+        plot=True,
+    )
+
+    return (ess > 50) and (idx < len(simulation_data) * 0.5)
diff --git a/dimsim/compute/workflow.py b/dimsim/compute/workflow.py
index d863521..6f28b08 100644
--- a/dimsim/compute/workflow.py
+++ b/dimsim/compute/workflow.py
@@ -1,14 +1,19 @@
+import json
 import pathlib
 
 import parsl
 
 from dimsim.compute.apps import (
     minimize_energy,
+    prepare_openmm_simulation,
     prepare_openmm_system,
     prepare_packed_topology,
+    run_equilibration,
 )
 from dimsim.compute.jobs import get_job_paths, is_complete, make_job_id
 from dimsim.configs.compute.density import DensityConfig
+from dimsim.configs.compute.ensemble import Ensemble
+from dimsim.configs.compute.equilibration import EquilibrationConfig
 
 
 class SimulationWorkflow:
@@ -24,6 +29,11 @@ def submit(self, compute_config: DensityConfig):
         job_id = make_job_id(compute_config)
         job_dir = get_job_paths(self.base_dir, job_id)["root"]
 
+        pathlib.Path(job_dir).mkdir(exist_ok=True)
+
+        with open(f"{job_dir}/compute_config_{compute_config['tag']}.json", "w") as f:
+            f.write(json.dumps(compute_config, indent=4))
+
         if is_complete(self.base_dir, job_id):
             return None  # already done, skip
 
@@ -37,17 +47,32 @@ def submit(self, compute_config: DensityConfig):
         # 2. set up openmm system
         setup_future = prepare_openmm_system(pack_future, job_dir)
 
-        # 3 (for now ...) get minimized energy
-        minimize_future = minimize_energy(setup_future, job_dir)
-
-        # 3. run equilibration step
-        # 4. run "production" step
+        # 3. set up openmm simulation
+        simulation_future = prepare_openmm_simulation(setup_future, job_dir)
+
+        # TODO: How to wire settings for individual apps into the public-facing run()?
+        # 4 (for now ...) get minimized energy
+        minimize_future = minimize_energy(simulation_future, job_dir)
+
+        equilibration_future = run_equilibration(
+            compute_config=compute_config,
+            equilibration_config=EquilibrationConfig(
+                ensemble=Ensemble.NVT,
+                steps_per_iteration=1_000_000,
+                step_size=1.0,
+            ),
+            minimization_future=minimize_future,
+            job_dir=job_dir,
+        )
+
+        # 1. run equilibration step
+        # 1. run "production" step
         # sim_future = run_simulation(config_future, job_dir)
-        # 5. analyze trajectory
-        # 6. check for convergence, if not converged, run more production and repeat
+        # 1. analyze trajectory
+        # 1. check for convergence, if not converged, run more production and repeat
         # analysis_future = analyze_trajectory(sim_future, job_dir)
 
-        return {"job_id": job_id, "future": minimize_future}
+        return {"job_id": job_id, "future": equilibration_future}
 
     def submit_batch(self, compute_configs: list[DensityConfig]):
         """Submit many jobs, skipping already-complete ones."""
diff --git a/dimsim/configs/compute/density.py b/dimsim/configs/compute/density.py
index b14c737..4ee5266 100644
--- a/dimsim/configs/compute/density.py
+++ b/dimsim/configs/compute/density.py
@@ -1,5 +1,6 @@
 import typing
 
+from dimsim.configs.compute.minimization import MinimizationConfig
 from dimsim.configs.targets.thermo import DataEntry
 
 
@@ -12,6 +13,8 @@ class DensityConfig(typing.TypedDict):
 
     n_molecules: int
 
+    minimization_config: MinimizationConfig
+
     """
-    Maybe add an RNG seed?
+    Maybe add an RNG seed? - this would be wrapped into equilibration and/or production MD runs
     """
diff --git a/dimsim/configs/compute/ensemble.py b/dimsim/configs/compute/ensemble.py
new file mode 100644
index 0000000..0364140
--- /dev/null
+++ b/dimsim/configs/compute/ensemble.py
@@ -0,0 +1,6 @@
+from enum import Enum
+
+
+class Ensemble(Enum):
+    NVT = "nvt"
+    NPT = "npt"
diff --git a/dimsim/configs/compute/equilibration.py b/dimsim/configs/compute/equilibration.py
new file mode 100644
index 0000000..2f8a0b2
--- /dev/null
+++ b/dimsim/configs/compute/equilibration.py
@@ -0,0 +1,11 @@
+import typing
+
+from dimsim.configs.compute.ensemble import Ensemble
+
+
+class EquilibrationConfig(typing.TypedDict):
+    ensemble: Ensemble
+
+    steps_per_iteration: int
+
+    step_size: float
diff --git a/dimsim/configs/compute/minimization.py b/dimsim/configs/compute/minimization.py
new file mode 100644
index 0000000..67164f5
--- /dev/null
+++ b/dimsim/configs/compute/minimization.py
@@ -0,0 +1,15 @@
+import typing
+
+
+class MinimizationConfig(typing.TypedDict):
+    tolerance: float
+    """Energy tolerance, passed directly to LocalEnergyMinimizer.minimize()"""
+
+    max_iterations: int
+    """Maximum number of iterations, passed directly to LocalEnergyMinimizer.minimize()"""
+
+
+default_minimization_config = MinimizationConfig(
+    tolerance=10.0,  # kJ/mol
+    max_iterations=0,
+)
diff --git a/examples/run_density.py b/examples/run_density.py
index d4822a0..ff6579b 100644
--- a/examples/run_density.py
+++ b/examples/run_density.py
@@ -1,6 +1,7 @@
 from dimsim.compute.configs import local_config, slurm_config
 from dimsim.compute.workflow import SimulationWorkflow
 from dimsim.configs.compute.density import DensityConfig
+from dimsim.configs.compute.minimization import MinimizationConfig
 from dimsim.datasets.thermoml import ThermoMLDataSet
 
 dataset = ThermoMLDataSet.from_xml(open("dimsim/_tests/data/thermoml/single_density.xml").read())
@@ -8,13 +9,17 @@
 job_specs = list()
 
 for target in dataset.properties:
-    for extra_n_molecules in range(20):
+    for extra_n_molecules in range(0, 20, 10):
         job_specs.append(
             DensityConfig(
                 tag="density",
                 target=target,
                 force_field="openff-2.3.0.offxml",
                 n_molecules=200 + extra_n_molecules,
+                minimization_config=MinimizationConfig(
+                    tolerance=0.0,
+                    max_iterations=100,
+                ),
             )
         )
 
diff --git a/pixi.lock b/pixi.lock
index cc6520a..3a385d0 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,433 +1,203 @@
-version: 6
+version: 7
+platforms:
+- name: linux-64
+- name: osx-arm64
 environments:
   default:
     channels:
     - url: https://conda.anaconda.org/conda-forge/
     indexes:
     - https://pypi.org/simple
-    options:
-      pypi-prerelease-mode: if-necessary-or-explicit
     packages:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.5-py312h5d8c7f2_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ambertools-23.3-py312h1577c9a_6.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py312h4c3975b_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/arpack-3.8.0-nompi_h0baa96a_101.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.3.0-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/asyncache-0.3.1-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.0-h92a005d_16.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.2-he7b75e1_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.4-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h92c474e_6.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.5-h0c2b49e_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.2-hee85082_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.21.0-h1d8da38_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.1-h46c1de9_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.8.3-h9cdc349_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h92c474e_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h92c474e_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.32.10-h186f887_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.510-h379b65b_14.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.14.0-h5cfcd09_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.10.0-h113e628_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.13.0-h3cf044e_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.8.0-h736e048_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.12.0-ha633028_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-with-css-6.3.0-hbca2aae_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/blinker-1.9.0-pyhff2d567_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.14.1-py312h5d8c7f2_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.9.3-hef928c7_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.1-h8b1a151_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.7-h28f887f_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.7-ha8fc4e3_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.23.3-hdaf4b65_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.13.3-hc63082f_11.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.3-h06ab39a_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.7-h8b1a151_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.35.4-h8824e59_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.606-h20b40b1_10.conda
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+  - sphinx-copybutton ; extra == 'docs'
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+  - ruamel-yaml ; extra == 'test'
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+  - strict-rfc3339 ; extra == 'test'
+  - werkzeug ; extra == 'test'
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+  requires_python: '>=3.10'
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+  requires_dist:
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+  - mypy ; extra == 'dev'
+  - flake8 ; extra == 'dev'
+  - flake8-annotations ; extra == 'dev'
+  - flake8-bandit ; extra == 'dev'
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+  - flake8-commas ; extra == 'dev'
+  - flake8-comprehensions ; extra == 'dev'
+  - flake8-continuation ; extra == 'dev'
+  - flake8-datetimez ; extra == 'dev'
+  - flake8-docstrings ; extra == 'dev'
+  - flake8-import-order ; extra == 'dev'
+  - flake8-literal ; extra == 'dev'
+  - flake8-modern-annotations ; extra == 'dev'
+  - flake8-noqa ; extra == 'dev'
+  - flake8-pyproject ; extra == 'dev'
+  - flake8-requirements ; extra == 'dev'
+  - flake8-typechecking-import ; extra == 'dev'
+  - flake8-use-fstring ; extra == 'dev'
+  - pep8-naming ; extra == 'dev'
+  requires_python: '>=3.7'
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+  name: jupyter-core
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+  requires_dist:
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+  - traitlets>=5.3
+  - intersphinx-registry ; extra == 'docs'
+  - myst-parser ; extra == 'docs'
+  - pydata-sphinx-theme ; extra == 'docs'
+  - sphinx-autodoc-typehints ; extra == 'docs'
+  - sphinxcontrib-spelling ; extra == 'docs'
+  - traitlets ; extra == 'docs'
+  - ipykernel ; extra == 'test'
+  - pre-commit ; extra == 'test'
+  - pytest-cov ; extra == 'test'
+  - pytest-timeout ; extra == 'test'
+  - pytest<9 ; extra == 'test'
+  requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/e9/87/b0667ede418386ab631e48924b845d326f366d61e6bd08fe68a748fae4d4/virtualenv-21.5.0-py3-none-any.whl
+  name: virtualenv
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+  - python-discovery>=1.4.2
+  - typing-extensions>=4.13.2 ; python_full_version < '3.11'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/eb/6c/6fcde0c8f616ed360ffd3587f7db9e225a7e62b583a04494d2f069cf64ea/jupyter_events-0.12.1-py3-none-any.whl
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+  - packaging
+  - python-json-logger>=2.0.4
+  - pyyaml>=5.3
+  - referencing
+  - rfc3339-validator
+  - rfc3986-validator>=0.1.1
+  - traitlets>=5.3
+  - click ; extra == 'cli'
+  - rich ; extra == 'cli'
+  - jupyterlite-sphinx ; extra == 'docs'
+  - myst-parser ; extra == 'docs'
+  - pydata-sphinx-theme>=0.16 ; extra == 'docs'
+  - sphinx>=8 ; extra == 'docs'
+  - sphinxcontrib-spelling ; extra == 'docs'
+  - click ; extra == 'test'
+  - pre-commit ; extra == 'test'
+  - pytest-asyncio>=0.19.0 ; extra == 'test'
+  - pytest-console-scripts ; extra == 'test'
+  - pytest>=7.0 ; extra == 'test'
+  - rich ; extra == 'test'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/ed/c9/d7977eaacb9df673210491da99e6a247e93df98c715fc43fd136ce1d3d33/arrow-1.4.0-py3-none-any.whl
+  name: arrow
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+  requires_dist:
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+  - backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
+  - tzdata ; python_full_version >= '3.9'
+  - doc8 ; extra == 'doc'
+  - sphinx>=7.0.0 ; extra == 'doc'
+  - sphinx-autobuild ; extra == 'doc'
+  - sphinx-autodoc-typehints ; extra == 'doc'
+  - sphinx-rtd-theme>=1.3.0 ; extra == 'doc'
+  - dateparser==1.* ; extra == 'test'
+  - pre-commit ; extra == 'test'
+  - pytest ; extra == 'test'
+  - pytest-cov ; extra == 'test'
+  - pytest-mock ; extra == 'test'
+  - pytz==2025.2 ; extra == 'test'
+  - simplejson==3.* ; extra == 'test'
+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/ef/af/4fbc8cab944db5d21b7e2a5b8e9211a03a79852b1157e2c102fcc61ac440/pandocfilters-1.5.1-py2.py3-none-any.whl
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+  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*'
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+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/f1/70/ba4b949bdc0490ab78d545459acd7702b211dfccf7eb89bbc1060f52818d/patsy-1.0.2-py2.py3-none-any.whl
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+  - pytest ; extra == 'test'
+  - pytest-cov ; extra == 'test'
+  - scipy ; extra == 'test'
+  requires_python: '>=3.6'
+- pypi: https://files.pythonhosted.org/packages/f1/7b/ce1eafaf1a76852e2ec9b22edecf1daa58175c090266e9f6c64afcd81d91/stack_data-0.6.3-py3-none-any.whl
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+  - typeguard ; extra == 'tests'
+  - pygments ; extra == 'tests'
+  - littleutils ; extra == 'tests'
+  - cython ; extra == 'tests'
+- pypi: https://files.pythonhosted.org/packages/f4/1e/2c9096fc19d5fd084b0184ca2b651e659aa0a37e6fdbecf6ece47f147fe1/rpds_py-2026.5.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  name: rpds-py
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+  requires_python: '>=3.11'
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+  name: webencodings
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+- pypi: https://files.pythonhosted.org/packages/f6/eb/9a8da295d26369746f2882ae9de425be2ecf507bb3c4d90713b3d60a6730/red_molsim-0.1.4-py3-none-any.whl
+  name: red-molsim
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+  requires_dist:
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+  - numpy>=1.20.0
+  - scipy>=1.6.0
+  - matplotlib>=3.3.0
+  - statsmodels>=0.12.0
+  - numba>=0.52.0
+  - mypy ; extra == 'dev'
+  - pytest>=6.1.2 ; extra == 'dev'
+  - pytest-runner ; extra == 'dev'
+  - pytest-env ; extra == 'dev'
+  - ruff ; extra == 'dev'
+  - pre-commit ; extra == 'dev'
+  - types-pyyaml ; extra == 'dev'
+  - mkdocs ; extra == 'dev'
+  - mkdocs-material ; extra == 'dev'
+  - mkdocs-gen-files ; extra == 'dev'
+  - mkdocs-literate-nav ; extra == 'dev'
+  - mkdocs-jupyter ; extra == 'dev'
+  - mkdocstrings ; extra == 'dev'
+  - mkdocstrings-python ; extra == 'dev'
+  - black ; extra == 'dev'
+  - mike ; extra == 'dev'
+  - mkdocs-bibtex ; extra == 'dev'
+  - build ; extra == 'dev'
+  - twine ; extra == 'dev'
+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/f8/9b/c108cdb55560eaf253f0cbdb61b29971e9fb34d9c3499b0e96e4e60ed8a5/pyzmq-27.1.0-cp312-abi3-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl
+  name: pyzmq
+  version: 27.1.0
+  sha256: 43ad9a73e3da1fab5b0e7e13402f0b2fb934ae1c876c51d0afff0e7c052eca31
+  requires_dist:
+  - cffi ; implementation_name == 'pypy'
+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/f9/33/bd5b9137445ea4b680023eb0469b2bb969d61303dedb2aac6560ff3d14a1/notebook_shim-0.2.4-py3-none-any.whl
+  name: notebook-shim
+  version: 0.2.4
+  sha256: 411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef
+  requires_dist:
+  - jupyter-server>=1.8,<3
+  - pytest ; extra == 'test'
+  - pytest-console-scripts ; extra == 'test'
+  - pytest-jupyter ; extra == 'test'
+  - pytest-tornasync ; extra == 'test'
+  requires_python: '>=3.7'
diff --git a/pixi.toml b/pixi.toml
index 7409814..6396f4f 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -11,22 +11,27 @@ run_tests = "python -m pytest -v --cov=dimsim --cov-config=pyproject.toml --cov-
 pydantic = "=2"
 pyyaml = "*"
 numpy = "*"
+polars = "*"
 setuptools_scm = "*"
 openff-toolkit = "0.18.*"
-openff-interchange = "0.5.*"
+openff-interchange = ">=0.5.2"
 openff-nagl-base = "*"
 openff-nagl-models = "*"
 openmm = "8.4.*"
 openmmtools = "*"
-rdkit = "2023.*"
+rdkit = "*"
 sqlmodel = "*"
 pytorch = "*"
-smee = "*"
+smee-base = "*"
 descent = "*"
 dask = "*"
 dask-jobqueue = "*"
 dask-kubernetes = "*"
 distributed = "*"
+# shim for upstream incompatibilities
+# https://github.com/huggingface/datasets/issues/7742
+# pyarrow <21 might also work
+datasets = ">=2.20"
 
 [pypi-dependencies]
 rdkit-stubs = "*"
@@ -41,11 +46,15 @@ dev = [ "py312", "openeye", "test", "typing", "dev" ]
 
 [feature.dev.dependencies]
 openff-packmol = "0.1.*"
+packmol = "*"
 pymol-open-source = "*"
 
 [feature.dev.pypi-dependencies]
 pre-commit = "*"
+ipython = "*"
 parsl = "*"
+jupyterlab = "*"
+red-molsim = "*"
 
 [feature.openeye]
 channels = [ "openeye", "conda-forge" ]