diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp
index d0d0b4d499..2bc2e5e773 100644
--- a/source/rrRoadRunner.cpp
+++ b/source/rrRoadRunner.cpp
@@ -1621,6 +1621,7 @@ namespace rr {
                                                << "conserved moieties";
                 }
             }
+            getSteadyStateSolver()->setValue("auto_moiety_analysis", true);
         }
 
         metabolicControlCheck(impl->model.get());
@@ -1707,6 +1708,8 @@ namespace rr {
             // restore original reload value
             self.loadOpt.modelGeneratorOpt = savedOpt;
         }
+        getSteadyStateSolver()->setValue("auto_moiety_analysis", false);
+
     }