diff --git a/pixi.lock b/pixi.lock
index c8af0d7..2b8a679 100644
--- a/pixi.lock
+++ b/pixi.lock
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+      - pypi: https://files.pythonhosted.org/packages/df/95/bdd01bbd523a63b113407c34c99af8495daa4651757cc28f3fabc393d131/stjames-0.0.237-py3-none-any.whl
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+      - pypi: https://files.pythonhosted.org/packages/df/95/bdd01bbd523a63b113407c34c99af8495daa4651757cc28f3fabc393d131/stjames-0.0.237-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl
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@@ -820,7 +820,7 @@ packages:
   name: rowan-python
   requires_dist:
   - httpx
-  - stjames>=0.0.236
+  - stjames>=0.0.237
   - setuptools
   - rdkit
   - nest-asyncio
@@ -1706,17 +1706,6 @@ packages:
   version: 2.3.0
   sha256: f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/d0/fb/be7d2e16e6c6143cd6834cd488d990d75352a5c9cdad6d5c615b5f01d736/stjames-0.0.236-py3-none-any.whl
-  name: stjames
-  version: 0.0.236
-  sha256: ea1459a5d0e0ccd206e5a387b201beec5e60ad6bc4f15dbcf649e2d4667fc40c
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl
   name: colorama
   version: 0.4.6
@@ -1803,6 +1792,17 @@ packages:
   - mkdocs-section-index ; extra == 'docs'
   - mkdocs-literate-nav ; extra == 'docs'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/df/95/bdd01bbd523a63b113407c34c99af8495daa4651757cc28f3fabc393d131/stjames-0.0.237-py3-none-any.whl
+  name: stjames
+  version: 0.0.237
+  sha256: 790c32bdc829efe52b7ccc442083d0d95fc01587d4063a08ea73cd9f686f6d21
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl
   name: packaging
   version: '26.2'
diff --git a/pyproject.toml b/pyproject.toml
index a9b47bd..926759f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.236",
+    "stjames>=0.0.237",
     "setuptools",
     "rdkit",
     "nest-asyncio",
diff --git a/rowan/__init__.py b/rowan/__init__.py
index 0bcf357..461b81c 100644
--- a/rowan/__init__.py
+++ b/rowan/__init__.py
@@ -3,6 +3,7 @@
 from stjames import (
     Atom,
     BandStructure,
+    Binder,
     BindingPoseContact,
     HydrationBridgeResidue,
     HydrationSite,
diff --git a/rowan/workflows/pose_analysis_md.py b/rowan/workflows/pose_analysis_md.py
index 2d85433..6afe99c 100644
--- a/rowan/workflows/pose_analysis_md.py
+++ b/rowan/workflows/pose_analysis_md.py
@@ -62,7 +62,7 @@ def trajectories(self) -> list[TrajectoryResult]:
         return [
             TrajectoryResult(
                 uuid=t.uuid,
-                ligand_rmsd=t.ligand_rmsd,
+                ligand_rmsd=t.binder_rmsd,
                 contacts=t.contacts,
                 sasa=t.sasa,
                 polar_sasa=t.polar_sasa,
diff --git a/rowan/workflows/protein_md.py b/rowan/workflows/protein_md.py
index e286ced..dbac958 100644
--- a/rowan/workflows/protein_md.py
+++ b/rowan/workflows/protein_md.py
@@ -4,7 +4,7 @@
 from pathlib import Path
 
 import stjames
-from stjames import GreedyClusteringSettings, KMeansClusteringSettings
+from stjames import Binder, GreedyClusteringSettings, KMeansClusteringSettings
 
 from ..folder import Folder
 from ..protein import Protein, retrieve_protein
@@ -171,6 +171,10 @@ def submit_protein_md_workflow(
     ionic_strength_M: float = 0.0,
     water_buffer: float = 10.0,
     save_solvent: bool = False,
+    num_solvent_to_save: int | None = None,
+    binder: Binder | None = None,
+    protein_restraint_cutoff: float | None = None,
+    protein_restraint_constant: float = 100,
     analysis_interval_ps: float | None = None,
     clustering: KMeansClusteringSettings | GreedyClusteringSettings | None = None,
     validate_forcefield: bool = True,
@@ -198,6 +202,16 @@ def submit_protein_md_workflow(
     :param ionic_strength_M: ionic strength of the solution, in M (molar)
     :param water_buffer: amount of water to add around the protein, in A
     :param save_solvent: whether solvent should be saved
+    :param num_solvent_to_save: keep this many solvent molecules nearest the binder, or all if None;
+        only meaningful when save_solvent is True and a binder is present
+    :param binder: optional binder specification (protein chains and/or small molecules).
+        When set, per-frame MM/GBSA scores are computed against the whole binder.
+        Per-frame binder RMSD is populated only when the binder is a single component
+        (one small molecule → heavy-atom RMSD; one binder chain → backbone N/CA/C/O RMSD);
+        it is empty for multi-molecule, multi-chain, or combined chain+molecule binders.
+    :param protein_restraint_cutoff: cutoff distance from the binder past which Cα atoms are
+        harmonically restrained, in Å; None disables restraints
+    :param protein_restraint_constant: force constant for Cα backbone restraints, in kcal/mol/Ų
     :param analysis_interval_ps: Interval at which to compute per-frame SASA and polar SASA, in ps.
         None disables those analyses.
     :param clustering: How to cluster trajectory frames. None disables clustering; pass a
@@ -222,7 +236,14 @@ def submit_protein_md_workflow(
         protein = protein.uuid
 
     if validate_forcefield:
-        Protein(uuid=protein).validate_protein_forcefield()
+        exclude_residue_names = (
+            [name for name in binder.small_molecules if isinstance(name, str)]
+            if binder is not None and binder.small_molecules
+            else None
+        )
+        Protein(uuid=protein).validate_protein_forcefield(
+            exclude_residue_names=exclude_residue_names
+        )
 
     workflow = stjames.ProteinMolecularDynamicsWorkflow(
         protein=protein,
@@ -238,6 +259,10 @@ def submit_protein_md_workflow(
         ionic_strength_M=ionic_strength_M,
         water_buffer=water_buffer,
         save_solvent=save_solvent,
+        num_solvent_to_save=num_solvent_to_save,
+        binder=binder,
+        protein_restraint_cutoff=protein_restraint_cutoff,
+        protein_restraint_constant=protein_restraint_constant,
         analysis_interval_ps=analysis_interval_ps,
         clustering=clustering,
     )