diff --git a/Yank/multistate/multistatereporter.py b/Yank/multistate/multistatereporter.py
index 9bc2296b..a7d5022c 100644
--- a/Yank/multistate/multistatereporter.py
+++ b/Yank/multistate/multistatereporter.py
@@ -1438,7 +1438,8 @@ def _calculate_checkpoint_iteration(self, iteration):
          """
         checkpoint_index, remainder = divmod(iteration, self._checkpoint_interval)
         if remainder == 0:
-            return checkpoint_index
+            # NetCDF variables can't be assigned using numpy integers.
+            return int(checkpoint_index)
         return None
 
     def _map_iteration_to_good(self, iteration):