diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index 40637c4..8adf5a1 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -114,6 +114,7 @@ def __init__(self, system, config):
 
             _logger.info("Applying SOMD1 perturbation compatibility.")
             self._system = _make_compatible(self._system)
+            self._system = _morph.link_to_reference(self._system)
 
             # Next, swap the water topology so that it is in AMBER format.