diff --git a/src/cltools/CLTool.h b/src/cltools/CLTool.h
index 5e990f653b1f598e1170ba47ee09a1d6ae528234..1d81b035d8c79010aac60c233a2ea8f3216fa961 100644
--- a/src/cltools/CLTool.h
+++ b/src/cltools/CLTool.h
@@ -24,8 +24,8 @@
 #include "core/CLTool.h"
 namespace PLMD{
 namespace cltools{
-// Ideally core/Colvar.h should be moved to this directory and Colvar should stay in namespace PLMD::colvar
-// With this trick, PLMD::CLToolMain is visible as PLMD::cltools::CLToolMain
+// Ideally core/CLTool.h should be moved to this directory and CLTool should stay in namespace PLMD::cltools
+// With this trick, PLMD::CLTool is visible as PLMD::cltools::CLTool
   using PLMD::CLTool;
 }
 }
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index f1012a26f64c6bea8dcbe8e63ba3fc7888b0ed71..8c5b20d05e9f9002d95ae080a364f4a9cb0ddc0b 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -34,7 +34,8 @@
 #include "tools/PDB.h"
 
 using namespace std;
-using namespace PLMD;
+
+namespace PLMD {
 
 ActionAtomistic::~ActionAtomistic(){
 // forget the pending request
@@ -280,3 +281,5 @@ void ActionAtomistic::makeWhole(){
     second=first+pbcDistance(first,second);
   }
 }
+
+}