diff --git a/src/somd2/runner/_repex.py b/src/somd2/runner/_repex.py
index 058e028..fe7b34b 100644
--- a/src/somd2/runner/_repex.py
+++ b/src/somd2/runner/_repex.py
@@ -309,6 +309,22 @@ def _create_dynamics(
             ):
                 from openmm.unit import angstrom
 
+                # Get the positions from the context.
+                positions = (
+                    dynamics.context()
+                    .getState(getPositions=True)
+                    .getPositions(asNumpy=True)
+                ) / angstrom
+
+                # The positions array also contains the ghost water atoms that
+                # were added during the GCMC setup. We need to make sure that
+                # we copy these over to the perturbed positions array.
+                diff = len(positions) - len(perturbed_positions)
+                if diff != 0:
+                    perturbed_positions = _np.concatenate(
+                        [perturbed_positions, positions[-diff:]]
+                    )
+
                 dynamics.context().setPeriodicBoxVectors(*perturbed_box * angstrom)
                 dynamics.context().setPositions(perturbed_positions * angstrom)