From 4dd153ab78105d5fa3e047d358f4669807c8ab2c Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Tue, 4 Aug 2026 18:59:02 +0100
Subject: [PATCH] Backport fix from PR #189. [ci skip]

---
 src/somd2/runner/_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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: