diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index d316644e15..275463f4de 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -298,6 +298,7 @@ void CreateBonds::many()
       }
     }
   }
+  neighbor->init();
 
   // recount bonds
 
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index c52e3a0441..9c50839c4a 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -420,6 +420,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
       break;
     }
   }
+  neighbor->init();
 }
 
 /* ----------------------------------------------------------------------