diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index 70a0313..0620f82 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -186,16 +186,16 @@ def __init__(self, system, config):
         if self._config.charge_difference != charge_diff:
             _logger.warning(
                 f"The charge difference of {charge_diff} between the end states "
-                f"does not match the expected value of {self._config.charge_difference}. "
-                "Please specify the 'charge_difference' if you wish to keep the charge "
-                "constant."
+                f"does not match the specified value of {self._config.charge_difference}."
             )
 
+        # The user value takes precedence.
+        if self._config.charge_difference != 0:
+            charge_diff = self._config.charge_difference
+
         # Create alchemical ions.
         if self._config.charge_difference != 0:
-            self._system = self._create_alchemical_ions(
-                self._system, self._config.charge_difference
-            )
+            self._system = self._create_alchemical_ions(self._system, charge_diff)
 
         # Set the lambda values.
         if self._config.lambda_values: