diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 4b3ef03..eff76db 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -1533,7 +1533,7 @@ def _check_restart(self):
                         raise ValueError(msg)
 
                 # Store the system to the list.
-                systems[i] = _sr.morph.link_to_perturbed(system)
+                systems[i] = _sr.morph.link_to_reference(system)
 
         # If this is a GCMC simulation, then remove all ghost waters from each of the systems.
         if self._config.gcmc: