diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 5066558..2558574 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -172,7 +172,8 @@ def __init__(self, system, config):
 
         # Make sure the system contains perturbable molecules.
         try:
-            self._system.molecules("property is_perturbable")
+            atoms = self._system["property is_perturbable"].atoms()
+            pert_idxs = self._system.atoms().find(atoms)
         except KeyError:
             msg = "No perturbable molecules in the system"
             _logger.error(msg)
@@ -265,7 +266,18 @@ def __init__(self, system, config):
             from ghostly import modify
 
             _logger.info("Applying modifications to ghost atom bonded terms")
-            self._system, self._modifications = modify(self._system)
+            try:
+                self._system, self._modifications = modify(self._system)
+            # Angle optimisation can sometimes fail.
+            except Exception as e1:
+                try:
+                    self._system, self._modifications = modify(
+                        self_system, optimise_angles=False
+                    )
+                except Exception as e2:
+                    msg = f"Unable to apply modifications to ghost atom bonded terms: {e1}; {e2}"
+                    _logger.error(msg)
+                    raise RuntimeError(msg)
 
         # Check for a periodic space.
         self._has_space = self._check_space()
@@ -363,6 +375,7 @@ def __init__(self, system, config):
         from math import isclose
 
         # Set the REST2 scale factors.
+        is_rest2 = False
         if self._config.rest2_scale is not None:
             # Single value. Interpolate between 1.0 at the end states and rest2_scale
             # at lambda = 0.5.
@@ -396,6 +409,45 @@ def __init__(self, system, config):
                         raise ValueError(msg)
                 self._rest2_scale_factors = self._config.rest2_scale
 
+            # If there are any non-zero REST2 scale factors, then log it.
+            if any(
+                not isclose(factor, 1.0, abs_tol=1e-4)
+                for factor in self._rest2_scale_factors
+            ):
+                is_rest2 = True
+                _logger.info(f"REST2 scaling factors: {self._rest2_scale_factors}")
+
+        # Make sure the REST2 selection is valid.
+        if self._config.rest2_selection is not None:
+
+            try:
+                atoms = _sr.mol.selection_to_atoms(
+                    self._system, self._config.rest2_selection
+                )
+            except:
+                msg = "Invalid 'rest2_selection' value."
+                _logger.error(msg)
+                raise ValueError(msg)
+
+            # Make sure the user hasn't selected all atoms.
+            if len(atoms) == self._system.num_atoms():
+                msg = "REST2 selection cannot contain all atoms in the system."
+                _logger.error(msg)
+                raise ValueError(msg)
+
+            # Get the atom indices.
+            idxs = self._system.atoms().find(atoms)
+
+            # If no indices are in the perturbable region, then add them.
+            if not any(i in pert_idxs for i in idxs):
+                idxs = sorted(pert_idxs + idxs)
+        else:
+            idxs = pert_idxs
+
+        # Log the atom indices in the REST2 selection.
+        if is_rest2:
+            _logger.info(f"REST2 selection contains {len(atoms)} atoms: {idxs}")
+
         # Apply hydrogen mass repartitioning.
         if self._config.hmr:
             # Work out the current hydrogen mass factor.
@@ -444,23 +496,6 @@ def __init__(self, system, config):
                         self._system, self._config.h_mass_factor
                     )
 
-        # Make sure the REST2 selection is valid.
-        if self._config.rest2_selection is not None:
-            from sire.mol import selection_to_atoms
-
-            try:
-                atoms = selection_to_atoms(self._system, self._config.rest2_selection)
-            except:
-                msg = "Invalid 'rest2_selection' value."
-                _logger.error(msg)
-                raise ValueError(msg)
-
-            # Make sure the user hasn't selected all atoms.
-            if len(atoms) == self._system.num_atoms():
-                msg = "REST2 selection cannot contain all atoms in the system."
-                _logger.error(msg)
-                raise ValueError(msg)
-
         # Flag whether this is a GPU simulation.
         self._is_gpu = self._config.platform in ["cuda", "opencl", "hip"]