diff --git a/CHANGELOG.md b/CHANGELOG.md
index f1578fa..d699ec4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ Changelog
 * Parallelise replica mixing [#181](https://github.com/OpenBioSim/somd2/pull/181).
 * Fixed the replica exchange GPU memory check querying the wrong device when `CUDA_VISIBLE_DEVICES` does not start at zero, since OpenMM numbers devices relative to the visible set whereas `pynvml` enumerates all of them [#183](https://github.com/OpenBioSim/somd2/issues/183).
 * Store GCMC sampling statistics per lambda value, converting those from earlier checkpoints on restart [#184](https://github.com/OpenBioSim/somd2/pull/184).
+* Link restart systems to the reference end state rather than the perturbed one, since that is the coordinate set that dynamics maintains. Perturbable molecules were otherwise resumed from the coordinates they were built with [#189](https://github.com/OpenBioSim/somd2/pull/189).
 
 [2026.1.0](https://github.com/openbiosim/somd2/compare/2025.1.0...2026.1.0) - Jun 2026
 --------------------------------------------------------------------------------------
diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 69da02d..158f176 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -1723,7 +1723,7 @@ 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: