diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 9cdf3b1abde4b541a94423f3cea7a5201d8d3eff..3542e402e5dfae5d4a733b8063794e7852cc4efb 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -22,7 +22,7 @@
 #include "Bias.h"
 #include "ActionRegister.h"
 #include "tools/Grid.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/File.h"
 
 
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 2f27842a46457aef87e05bf716f704881c6d82b1..e4a2f341cd173a532bcc23f07eb5e59185778e50 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -24,7 +24,7 @@
 #include "tools/Grid.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "core/FlexibleBin.h"
 #include "tools/Matrix.h"
 #include "tools/Random.h"
diff --git a/src/core/Action.cpp b/src/core/Action.cpp
index 13088fab7f5a26c7c9b6f6dff6343ee08b91f326..1fdd9e3d884bcfbc5c9a875def69d44c19b70c58 100644
--- a/src/core/Action.cpp
+++ b/src/core/Action.cpp
@@ -23,7 +23,7 @@
 #include "ActionWithValue.h"
 #include "PlumedMain.h"
 #include "tools/Log.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "Atoms.h"
 #include "ActionSet.h"
 #include <iostream>
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index b430a561ebc73f25dd4588173a40521f62af0643..c612cc0cfdd26e13e3719e606bd306d01a36fe23 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -27,7 +27,7 @@
 #include "ActionWithValue.h"
 #include "Colvar.h"
 #include "ActionWithVirtualAtom.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "Atoms.h"
 #include "tools/Pbc.h"
 #include "tools/PDB.h"
diff --git a/src/core/ActionSetup.cpp b/src/core/ActionSetup.cpp
index f7a333f178501350e88f3375b6347b275baeac6d..d11107c4c1e90f5ed9b62e1b0f0eeebfb6576884 100644
--- a/src/core/ActionSetup.cpp
+++ b/src/core/ActionSetup.cpp
@@ -22,7 +22,7 @@
 #include "ActionSetup.h"
 #include "PlumedMain.h"
 #include "ActionSet.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 namespace PLMD{
 
diff --git a/src/core/ActionWithValue.cpp b/src/core/ActionWithValue.cpp
index d09f53b3e502fa8eeeead68b70c2e82edc78cbd0..66616a5bc6b7825ea8b58677d90daf188d7ec3c3 100644
--- a/src/core/ActionWithValue.cpp
+++ b/src/core/ActionWithValue.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "ActionWithValue.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 namespace PLMD{
diff --git a/src/core/ActionWithValue.h b/src/core/ActionWithValue.h
index 15c03f59e888cfd404fc41f595263aae06a59b56..3c1769a048665f5ff1452a65102162dde5799c46 100644
--- a/src/core/ActionWithValue.h
+++ b/src/core/ActionWithValue.h
@@ -24,7 +24,7 @@
 
 #include "Action.h"
 #include "Value.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include <vector>
 
 namespace PLMD{
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index e70c6724c18a88ce3dd1b11f10aeea7f9ff3bd7e..ebff0c099585fb11480889d2a84995bd14d01776 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -25,7 +25,7 @@
 #include "tools/Communicator.h"
 #include "tools/Tensor.h"
 #include "tools/Units.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/AtomNumber.h"
 #include <vector>
 #include <set>
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index c69addd677f1905774890d5c4adf8766ce2f3ae3..0bcc864676144009415d3ed0b636278b78326215 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "config/Config.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/Communicator.h"
 #include "CLTool.h"
 #include "CLToolMain.h"
diff --git a/src/core/MDAtoms.cpp b/src/core/MDAtoms.cpp
index 431c946338bd5558063889ce526e43f035f18fcc..3bbccc75613e0aadadd9d4570c8e0d570f310ba6 100644
--- a/src/core/MDAtoms.cpp
+++ b/src/core/MDAtoms.cpp
@@ -23,7 +23,7 @@
 #include <string>
 #include "MDAtoms.h"
 #include "tools/Tools.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 592decf6d98815a32d2f5baa3b537d5d28df5173..20439f4ada2500856d46b70ae88fafc398ef4bfd 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -32,7 +32,7 @@
 #include <cstdlib>
 #include "ActionRegister.h"
 #include "GREX.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "Atoms.h"
 #include "ActionSet.h"
 #include "tools/Log.h"
diff --git a/src/core/PlumedMainInitializer.cpp b/src/core/PlumedMainInitializer.cpp
index d554ee0ff335f15b98a5e8e3025396ef15f36c69..4c3e24d72f2c7c418619ea279170fed1e14492b8 100644
--- a/src/core/PlumedMainInitializer.cpp
+++ b/src/core/PlumedMainInitializer.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "PlumedMain.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include <cstdlib>
 
 using namespace std;
diff --git a/src/core/SetupMolInfo.h b/src/core/SetupMolInfo.h
index 09ec126024c2cc61de0177b7f0693d173acfcae7..95276925e308527c3b03ef4745f8abfd3e1e99d1 100644
--- a/src/core/SetupMolInfo.h
+++ b/src/core/SetupMolInfo.h
@@ -24,7 +24,7 @@
 
 #include "ActionSetup.h"
 #include "ActionAtomistic.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 namespace PLMD {
 
diff --git a/src/core/Value.cpp b/src/core/Value.cpp
index e1940025ca7a891b1423b5a8c05193eadfa1fb63..1b3d829329d0aaef2bbd61f249fbf954e317f2ea 100644
--- a/src/core/Value.cpp
+++ b/src/core/Value.cpp
@@ -24,7 +24,7 @@
 #include "ActionAtomistic.h"
 #include "ActionWithArguments.h"
 #include "ActionWithVirtualAtom.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "Atoms.h"
 #include "PlumedMain.h"
 
diff --git a/src/core/Value.h b/src/core/Value.h
index 03abb0f1e5262541b43a00e37734bff4c06f96b7..cc35f5d31dba970f0da9cf0ded7ffbe7bae76fdd 100644
--- a/src/core/Value.h
+++ b/src/core/Value.h
@@ -25,7 +25,7 @@
 #include <vector>
 #include <string>
 #include <map>
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/Tools.h"
 #include "tools/AtomNumber.h"
 #include "tools/Vector.h"
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index e86dc9c99fbb9c2eaced534469006416fdda5282..0e61fa16312faeb304b52860cbe9cbb39fc27300 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -22,7 +22,7 @@
 #include "core/Action.h"
 #include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/imd/ActionIMD.cpp b/src/imd/ActionIMD.cpp
index c71f5ac38f3ecd16e70a90c7b16a99121084aece..0b3979fcf13e4f1259a20b4da6a571f3d1bca3e6 100644
--- a/src/imd/ActionIMD.cpp
+++ b/src/imd/ActionIMD.cpp
@@ -24,7 +24,7 @@
 #include "../core/ActionPilot.h"
 #include "../core/PlumedMain.h"
 #include "../core/Atoms.h"
-#include "../tools/PlumedException.h"
+#include "../tools/Exception.h"
 #include <unistd.h>
 
 extern "C" {
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index da4f2de988d413c2b65ec56e3b260c3636ace36b..1ef834d3b6b9c0ca8adc63dfd98cdf8e422f0474 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -22,7 +22,7 @@
 #include "core/ActionSetup.h"
 #include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/setup/Restart.cpp b/src/setup/Restart.cpp
index 7b8f4e426b48a991b9c0111ebafa95695f7c4d85..84bd2da77e1eea8da111ae3113c968a18ef5d33c 100644
--- a/src/setup/Restart.cpp
+++ b/src/setup/Restart.cpp
@@ -23,7 +23,7 @@
 #include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index 35683e339a0c90284fe8d8cce1e43406d820e500..479459c89a9c17ed2a88576da1e22ac5569949b2 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -23,7 +23,7 @@
 #include "core/ActionRegister.h"
 #include "core/PlumedMain.h"
 #include "core/Atoms.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/tools/AtomNumber.h b/src/tools/AtomNumber.h
index f72990a5b6ead05858d62bf132d7b862278f0167..3ebc4303a9ee87e7fa54b138a549d02ab66873bc 100644
--- a/src/tools/AtomNumber.h
+++ b/src/tools/AtomNumber.h
@@ -22,7 +22,7 @@
 #ifndef __PLUMED_tools_AtomNumber_h
 #define __PLUMED_tools_AtomNumber_h
 
-#include "PlumedException.h"
+#include "Exception.h"
 #include <limits>
 
 namespace PLMD{
diff --git a/src/tools/Citations.cpp b/src/tools/Citations.cpp
index 2618ec39dd94470871836f7c50aff05ac98a0917..1047a9b0497c148c11d5f9e9ce29971f6b765554 100644
--- a/src/tools/Citations.cpp
+++ b/src/tools/Citations.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Citations.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "Tools.h"
 #include <iostream>
 
diff --git a/src/tools/Communicator.cpp b/src/tools/Communicator.cpp
index 20159c9453aa0ef94f1cc1da1251b689614d52a4..1c94f0c77543f760824f0671496eabb65ad3048e 100644
--- a/src/tools/Communicator.cpp
+++ b/src/tools/Communicator.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include <cstdlib>
 #include "Communicator.h"
-#include "PlumedException.h"
+#include "Exception.h"
 
 using namespace std;
 
diff --git a/src/tools/Communicator.h b/src/tools/Communicator.h
index ad553c42a011b7b9d63650db213e3a0e661094ee..3caf3aade17fd538649f117b08e634ee45ad878b 100644
--- a/src/tools/Communicator.h
+++ b/src/tools/Communicator.h
@@ -25,7 +25,7 @@
 #include <mpi.h>
 #endif
 #include <cstdlib>
-#include "PlumedException.h"
+#include "Exception.h"
 
 namespace PLMD{
 
diff --git a/src/tools/DLLoader.cpp b/src/tools/DLLoader.cpp
index 59ab3b0813134a888cee4feea962620d990e885c..d26c77ed1b66e90846f8db84e6aa32f471bca64a 100644
--- a/src/tools/DLLoader.cpp
+++ b/src/tools/DLLoader.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "DLLoader.h"
-#include "PlumedException.h"
+#include "Exception.h"
 
 #ifdef __PLUMED_HAS_DLOPEN
 #include <dlfcn.h>
diff --git a/src/tools/PlumedException.cpp b/src/tools/Exception.cpp
similarity index 82%
rename from src/tools/PlumedException.cpp
rename to src/tools/Exception.cpp
index 6e606812687751b5bd7f70c1d34be4d97f8e9d3c..4462128895aeb826650a270867d1f99e0dacc08d 100644
--- a/src/tools/PlumedException.cpp
+++ b/src/tools/Exception.cpp
@@ -19,7 +19,7 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "PlumedException.h"
+#include "Exception.h"
 
 #if ! defined(__PLUMED_EXCEPTIONS)
 #include <execinfo.h>
@@ -29,9 +29,9 @@
 #include <cstdlib>
 
 using namespace std;
-using namespace PLMD;
+namespace PLMD{
 
-std::string PlumedException::format(const std::string&msg,const std::string&file,unsigned line,const std::string&function){
+std::string Exception::format(const std::string&msg,const std::string&file,unsigned line,const std::string&function){
   std::string message;
   message="\n+++ Internal PLUMED error";
   if(file.length()>0){
@@ -45,25 +45,25 @@ std::string PlumedException::format(const std::string&msg,const std::string&file
 }
 
 
-PlumedException::PlumedException()
+Exception::Exception()
 {
   this->msg=format("","",0,"");
   abortIfExceptionsAreDisabled();
 }
 
-PlumedException::PlumedException(const std::string&msg)
+Exception::Exception(const std::string&msg)
 {
   this->msg=format(msg,"",0,"");
   abortIfExceptionsAreDisabled();
 }
 
-PlumedException::PlumedException(const std::string&msg,const std::string&file,unsigned line,const std::string&function)
+Exception::Exception(const std::string&msg,const std::string&file,unsigned line,const std::string&function)
 {
   this->msg=format(msg,file,line,function);
   abortIfExceptionsAreDisabled();
 }
 
-void PlumedException::abortIfExceptionsAreDisabled(){
+void Exception::abortIfExceptionsAreDisabled(){
 #if ! defined(__PLUMED_EXCEPTIONS)
   fprintf(stderr,"%s",what());
   fprintf(stderr,"\n");
@@ -80,4 +80,6 @@ void PlumedException::abortIfExceptionsAreDisabled(){
 #endif
 }
 
+}
+
 
diff --git a/src/tools/PlumedException.h b/src/tools/Exception.h
similarity index 80%
rename from src/tools/PlumedException.h
rename to src/tools/Exception.h
index a7b85a9b2c9f12aae1583b000a29c773cd650a5c..b1c815a3b3b3654b3523f6b7ab036e9c882e8755 100644
--- a/src/tools/PlumedException.h
+++ b/src/tools/Exception.h
@@ -19,8 +19,8 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_tools_PlumedException_h
-#define __PLUMED_tools_PlumedException_h
+#ifndef __PLUMED_tools_Exception_h
+#define __PLUMED_tools_Exception_h
 
 #include <string>
 #include <stdexcept>
@@ -38,11 +38,11 @@ should be documented in some better way (e.g. printing parts of the manual in th
 
 To throw an error, just throw a c++ exception
 \verbatim
-  if(something_bad) throw PlumedException();
+  if(something_bad) throw Exception();
 \endverbatim
 or better add an error message to that
 \verbatim
-  if(something_bad) throw PlumedException("describe the error here);
+  if(something_bad) throw Exception("describe the error here);
 \endverbatim
 
 Even better, you can use the predefined macros 
@@ -87,7 +87,7 @@ even if I am not fully convinced that this is a good idea.
 Notice that sometime people claim that code compiled with exception enabled
 is slower (GB)
 */
-class PlumedException : public std::exception
+class Exception : public std::exception
 {
   std::string msg;
 /// Common tool, invoked by all the constructor to build the message string
@@ -96,15 +96,15 @@ class PlumedException : public std::exception
   void abortIfExceptionsAreDisabled();
 public:
 /// Without message
-  PlumedException();
+  Exception();
 /// With message
-  PlumedException(const std::string&);
+  Exception(const std::string&);
 /// With message plus file, line and function (meant to be used through a preprocessor macro)
-  PlumedException(const std::string&,const std::string&,unsigned,const std::string&);
+  Exception(const std::string&,const std::string&,unsigned,const std::string&);
 /// Returns the error message
   virtual const char* what() const throw(){return msg.c_str();}
 /// Destructor should be defined and should not throw other exceptions
-  virtual ~PlumedException() throw(){};
+  virtual ~Exception() throw(){};
 };
 
 // With GNU compiler, we can use __PRETTY_FUNCTION__ to get the function name
@@ -112,18 +112,18 @@ public:
 #define __PRETTY_FUNCTION__ ""
 #endif
 
-/// \relates PLMD::PlumedException
+/// \relates PLMD::Exception
 /// Just print file/line/function information and exit
-#define plumed_error() throw PLMD::PlumedException("",__FILE__,__LINE__,__PRETTY_FUNCTION__)
-/// \relates PLMD::PlumedException
+#define plumed_error() throw PLMD::Exception("",__FILE__,__LINE__,__PRETTY_FUNCTION__)
+/// \relates PLMD::Exception
 /// Print file/line/function information plus msg and exit
-#define plumed_merror(msg) throw PLMD::PlumedException(msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
-/// \relates PLMD::PlumedException
+#define plumed_merror(msg) throw PLMD::Exception(msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+/// \relates PLMD::Exception
 /// Conditionally print file/line/function information and exit
-#define plumed_assert(test) if(!(test)) throw PLMD::PlumedException("assertion failed " #test,__FILE__,__LINE__,__PRETTY_FUNCTION__)
-/// \relates PLMD::PlumedException
+#define plumed_assert(test) if(!(test)) throw PLMD::Exception("assertion failed " #test,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+/// \relates PLMD::Exception
 /// Conditionally print file/line/function information plus msg and exit
-#define plumed_massert(test,msg) if(!(test)) throw PLMD::PlumedException("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
+#define plumed_massert(test,msg) if(!(test)) throw PLMD::Exception("assertion failed " #test ", " msg,__FILE__,__LINE__,__PRETTY_FUNCTION__)
 
 }
 #endif
diff --git a/src/tools/FileBase.cpp b/src/tools/FileBase.cpp
index b9190df2acbc5e834ccc72b12a7749015e9f2088..467d1a93a0dd7ff63be8528cf19fdc336dfab598 100644
--- a/src/tools/FileBase.cpp
+++ b/src/tools/FileBase.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "File.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "core/Action.h"
 #include "core/PlumedMain.h"
 #include "core/Value.h"
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index 88820bf478618527208b50b2cc8ddb3fa088d395..f2c4d240d411c69d86906314818cb18f0fef4960 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -29,7 +29,7 @@
 #include "Tools.h"
 #include "core/Value.h"
 #include "File.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "KernelFunctions.h"
 
 using namespace std;
diff --git a/src/tools/HistogramBead.h b/src/tools/HistogramBead.h
index 39386524d82a0160216f00201b615f56d2e8e39a..db95661f2f54cef448158910166122476ed03fe8 100644
--- a/src/tools/HistogramBead.h
+++ b/src/tools/HistogramBead.h
@@ -25,7 +25,7 @@
 #include <cmath>
 #include <string>
 #include <vector>
-#include "PlumedException.h"
+#include "Exception.h"
 #include "Tools.h"
 
 namespace PLMD {
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index 2032cb0a4f57068916b98f5d6c1c04767172a664..e979d476a19043242eaf26e98b89b427e381c184 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "File.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "core/Action.h"
 #include "core/PlumedMain.h"
 #include "core/Value.h"
diff --git a/src/tools/Keywords.h b/src/tools/Keywords.h
index 6c3f428eddb2f895cd446b5e9a5bdb141de188b8..345d278ba0628a273972d1c34a37f55aa6e1abf1 100644
--- a/src/tools/Keywords.h
+++ b/src/tools/Keywords.h
@@ -26,7 +26,7 @@
 #include <set>
 #include <map>
 
-#include "PlumedException.h"
+#include "Exception.h"
 
 namespace PLMD{
 
diff --git a/src/tools/LatticeReduction.cpp b/src/tools/LatticeReduction.cpp
index 70b548f5cae4360f53becae4cbb61c12cdffdf07..a350535a85474743c074a96d469de52d7f42f3ae 100644
--- a/src/tools/LatticeReduction.cpp
+++ b/src/tools/LatticeReduction.cpp
@@ -19,7 +19,7 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "PlumedException.h"
+#include "Exception.h"
 #include "LatticeReduction.h"
 
 namespace PLMD{
diff --git a/src/tools/Matrix.h b/src/tools/Matrix.h
index 680cb5b944a20006db4820eebf604a3814549aa8..2e77465a76caa6b2c294966a7611bc3e69201272 100644
--- a/src/tools/Matrix.h
+++ b/src/tools/Matrix.h
@@ -25,7 +25,7 @@
 #include <string>
 #include <set>
 #include <cmath>
-#include "PlumedException.h"
+#include "Exception.h"
 #include "MatrixSquareBracketsAccess.h"
 #include "Log.h"
 
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index 0277288cdc327b823bb5b91ef8f1642e68912d76..9af38e84c2bccd1fab9bd5a7bf34abc023d3383a 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "File.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "core/Action.h"
 #include "core/PlumedMain.h"
 #include "core/Value.h"
diff --git a/src/tools/Pbc.cpp b/src/tools/Pbc.cpp
index 382b059f540d19db78d96be3d35ffbf0037d08ef..9a9f8e9a531f987f5b07ccb0fbd0117fabdb749f 100644
--- a/src/tools/Pbc.cpp
+++ b/src/tools/Pbc.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Pbc.h"
 #include "Tools.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "LatticeReduction.h"
 
 namespace PLMD{
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index 599962c10e7d86f9a061fa06c671c2d5c647beb1..1719399e5b70739650d8dd21410a52fe2dbe98cf 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -23,7 +23,7 @@
 #include "PDB.h"
 #include "Log.h"
 #include "OptimalAlignment.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include <cmath>
 #include <iostream>
 
diff --git a/src/tools/Stopwatch.cpp b/src/tools/Stopwatch.cpp
index 57d92745d4663554377bc612d63df839663d8853..7ea9c1c6f28db7e8582c63457153395e5ba0a79d 100644
--- a/src/tools/Stopwatch.cpp
+++ b/src/tools/Stopwatch.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 
 #include "Stopwatch.h"
-#include "PlumedException.h"
+#include "Exception.h"
 
 #include <cstdio>
 #include <iostream>
diff --git a/src/tools/Tensor.cpp b/src/tools/Tensor.cpp
index 0279cee036d21a873668107574a5c1c416e8c06e..12e504ace5a7ce04868bb1a82f6592ab1094d108 100644
--- a/src/tools/Tensor.cpp
+++ b/src/tools/Tensor.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Tensor.h"
-#include "PlumedException.h"
+#include "Exception.h"
 
 namespace PLMD{
 
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 438226eb9ee0d5a85922d9a361dac9b7018e137b..63fd48993303c158a3474670b0c262399ec86da5 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -22,7 +22,7 @@
 #include <iostream>
 #include "Tools.h"
 #include "AtomNumber.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include "File.h"
 #include <cstring>
 #include <dirent.h>
diff --git a/src/tools/Vector.cpp b/src/tools/Vector.cpp
index 6b8cee2bc70120f1368744816cf7cd989f4aa183..94c3efa06e5fab70f3246ccfe9349f1ca3538320 100644
--- a/src/tools/Vector.cpp
+++ b/src/tools/Vector.cpp
@@ -20,7 +20,7 @@
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "Vector.h"
-#include "PlumedException.h"
+#include "Exception.h"
 #include <cmath>
 
 namespace PLMD{
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index d3a48787711ca26686f0f87fd6bfa25a3bfe2bef..1d8475b48857302dd5c38da1984cdd66ddb0776c 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -22,7 +22,7 @@
 #include "ActionWithVirtualAtom.h"
 #include "ActionRegister.h"
 #include "tools/Vector.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 
 using namespace std;
 
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index 8428890667239a5d278517f7a8cf806282e50377..f6f536722333cf5259d05924700ba0c9325b8507 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -24,7 +24,7 @@
 
 #include "core/ActionWithValue.h"
 #include "core/ActionAtomistic.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/DynamicList.h"
 #include <vector>
 
diff --git a/src/vesselbase/Vessel.cpp b/src/vesselbase/Vessel.cpp
index 8721ef831915b61605716e7e7eaaa50053f8555b..a2fc3856a89afa4764c9160ac5027232e27feaf5 100644
--- a/src/vesselbase/Vessel.cpp
+++ b/src/vesselbase/Vessel.cpp
@@ -21,7 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "ActionWithVessel.h"
 #include "Vessel.h"
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "core/Value.h"
 #include "tools/Log.h"
 
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index bb3ffd30f741e8edf010ba2e7f57ec1a07060c33..fe083f6987198091621251d53c89f74db7f24148 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -25,7 +25,7 @@
 #include <string>
 #include <cstring>
 #include <vector>
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/Keywords.h"
 
 namespace PLMD{
diff --git a/src/vesselbase/VesselRegister.h b/src/vesselbase/VesselRegister.h
index 5d630f1c4dbb7f9c55907313d6646d9ecdab21c4..d65e3ab3b675044c1c9ebbdffc667f8336429561 100644
--- a/src/vesselbase/VesselRegister.h
+++ b/src/vesselbase/VesselRegister.h
@@ -26,7 +26,7 @@
 #include <cstring>
 #include <vector>
 #include <map>
-#include "tools/PlumedException.h"
+#include "tools/Exception.h"
 #include "tools/Keywords.h"
 
 namespace PLMD{