diff --git a/src/somd2/runner/_base.py b/src/somd2/runner/_base.py
index 4309ec7..44eb11e 100644
--- a/src/somd2/runner/_base.py
+++ b/src/somd2/runner/_base.py
@@ -264,7 +264,7 @@ def __init__(self, system, config):
             from ghostly import modify
 
             _logger.info("Applying modifications to ghost atom bonded terms")
-            self._system = modify(self._system)
+            self._system, self._modifications = modify(self._system)
 
         # Check for a periodic space.
         self._has_space = self._check_space()