diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index de44ed6..a2ba81c 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -617,6 +617,7 @@ def _compare_configs(config1, config2):
             "log_level",
             "log_file",
             "overwrite",
+            "timeout",
         ]
         for key in config1.keys():
             if key not in allowed_diffs: