diff --git a/src/somd2/runner/_repex.py b/src/somd2/runner/_repex.py
index 7a2c329..1453cec 100644
--- a/src/somd2/runner/_repex.py
+++ b/src/somd2/runner/_repex.py
@@ -336,11 +336,23 @@ def run(self):
         # Create the replica list.
         replica_list = list(range(self._config.num_lambda))
 
-        # Minimise at each lambda value. This is currently done in serial due to a
-        # threading issue with the Sire OpenMM minimiser.
+        # Minimise at each lambda value.
         if self._config.minimise:
-            for i in range(self._config.num_lambda):
-                self._minimise(i)
+            for i in range(num_batches):
+                with ThreadPoolExecutor(max_workers=num_workers) as executor:
+                    try:
+                        for success, index, e in executor.map(
+                            self._minimise,
+                            replica_list[i * num_workers : (i + 1) * num_workers],
+                        ):
+                            if not success:
+                                _logger.error(
+                                    f"Minimisation failed for {_lam_sym} = {self._lambda_values[index]:.5f}: {e}"
+                                )
+                                raise e
+                    except KeyboardInterrupt:
+                        _logger.error("Minimisation cancelled. Exiting.")
+                        exit(1)
 
         # Current block number.
         block = 0
@@ -545,12 +557,23 @@ def _minimise(self, index):
         """
         _logger.info(f"Minimising at {_lam_sym} = {self._lambda_values[index]:.5f}")
 
+        # Note: For now we minimise with the LocalEnergyMinimizer in OpenMM
+        # since dynamics.minimise() is not thread safe.
+
         try:
+            from openmm import LocalEnergyMinimizer
+
             # Get the dynamics object.
             dynamics = self._dynamics_cache.get(index)
 
-            # Minimise the system.
-            dynamics.minimise(timeout=self._config.timeout)
+            # Get the context.
+            context = dynamics.context()
+
+            # Minimise.
+            LocalEnergyMinimizer.minimize(context)
+
+            # Clear the internal dynamics state.
+            dynamics._d._clear_state()
 
         except Exception as e:
             return False, index, e