diff --git a/src/colvar/PathMSDBase.h b/src/colvar/PathMSDBase.h
index d289d19871c560ee7521b82e9bc5c9aac7d61d97..62e80ba17940c5c38e6cc5045e30c2791a81dfa1 100644
--- a/src/colvar/PathMSDBase.h
+++ b/src/colvar/PathMSDBase.h
@@ -34,8 +34,6 @@
 #include "tools/RMSD.h"
 #include "tools/Tools.h"
 
-using namespace std;
-
 namespace PLMD{
 namespace colvar{
 
@@ -46,13 +44,13 @@ class PathMSDBase : public Colvar {
         // cardinal indexing: needed to map over msd 
         unsigned index;
         // spiwok indexing
-        vector<double> property;
+        std::vector<double> property;
         // distance
         double distance;
         // similarity (exp - lambda distance) or other
         double similarity;
         // derivatives of the distance
-        vector<Vector> distder;
+        std::vector<Vector> distder;
         // here one can add a pointer to a value (hypothetically providing a distance from a point) 
   };
   struct imgOrderByDist {
@@ -70,16 +68,16 @@ class PathMSDBase : public Colvar {
   bool pbc;
   int neigh_size;
   double neigh_stride;
-  vector<RMSD> msdv;
-  string reference;
-  vector<Vector> derivs_s;
-  vector<Vector> derivs_z;
-  vector< vector <Vector> > derivs_v;
-  vector <ImagePath> imgVec; // this can be used for doing neighlist   
+  std::vector<RMSD> msdv;
+  std::string reference;
+  std::vector<Vector> derivs_s;
+  std::vector<Vector> derivs_z;
+  std::vector< std::vector <Vector> > derivs_v;
+  std::vector <ImagePath> imgVec; // this can be used for doing neighlist   
 protected:
-  vector<PDB> pdbv;
-  vector<string> labels;
-  vector< vector<double> > indexvec; // use double to allow isomaps
+  std::vector<PDB> pdbv;
+  std::vector<std::string> labels;
+  std::vector< std::vector<double> > indexvec; // use double to allow isomaps
   unsigned nframes;
 public:
   PathMSDBase(const ActionOptions&);
diff --git a/src/core/FlexibleBin.h b/src/core/FlexibleBin.h
index 9ee167890df5e6947b6a17b8b4a868d1c69bb9a5..158e8e437b7339f1923c43f8f9d491979a4370a6 100644
--- a/src/core/FlexibleBin.h
+++ b/src/core/FlexibleBin.h
@@ -23,7 +23,6 @@
 #define __PLUMED_core_FlexibleBin_h
 
 #include<vector>
-using namespace std;
 
 namespace PLMD{
 
@@ -36,17 +35,17 @@ class FlexibleBin{
 		ActionWithArguments *paction;
 		double sigma;	
 		// variance is the matrix that really matters
-		vector<double> variance;	
+		std::vector<double> variance;	
 		// this is only there
-		vector<double> average;
+		std::vector<double> average;
 	public:
 		/// a constructor that takes the pointer of the action that contains it
 		FlexibleBin(int type,ActionWithArguments *paction, double const &d);
 		~FlexibleBin();
 		/// update the average (always for diffusion) or calculate the geom covariance (  only when do_when_zero is zero)
 		void update(bool nowAddAHill );
-		vector<double> getMatrix() const;
-		vector<double> getInverseMatrix() const;
+		std::vector<double> getMatrix() const;
+		std::vector<double> getInverseMatrix() const;
 		enum AdaptiveHillsType { none, diffusion, geometry }; 
 };