diff --git a/.travis.yml b/.travis.yml
index aef80d6972b6e18675e09af49fc1c55ae71857fd..c64de44c71a311a3d7e6d29c83f07d5a2a918ec9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -72,7 +72,7 @@ install:
 # install doxygen-latex
   - if test "$MAKEDOC" == yes ; then sudo apt-get install -y doxygen-latex ; fi
 # then replace doxygen with the desided version
-  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_7 ; fi
+  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_11 ; fi
   - if test "$VALGRIND" == yes ; then sudo apt-get install -y valgrind           ; fi
   - if test "$LAPACK" == yes ; then sudo apt-get -y install libatlas-base-dev      ; fi
   - if test "$ALMOST" == yes ; then sudo apt-get -y install libatlas-base-dev      ; fi
@@ -90,7 +90,7 @@ script:
 # this is done only if PLUMED_CXX is defined
 # we have to pass the full path since on travis machines sudo does not have compilers in the path
   - if test "$PLUMED_CXX" ; then ./configure CXX=$(which $PLUMED_CXX) CC=$(which $PLUMED_CC) CXXFLAGS="$PLUMED_CXXFLAGS" LDFLAGS="$PLUMED_LDFLAGS" CPPFLAGS="$PLUMED_CPPFLAGS" $ENALMOST $CONFIG_FLAGS ; fi
-  - if test "$PLUMED_CXX" ; then make -j 2 ; fi
+  - if test "$PLUMED_CXX" ; then make -j 4 ; fi
 # we install plumed so that it is in the path
   - if test "$PLUMED_CXX" ; then make install prefix="$HOME/opt" ; fi
 
diff --git a/.travis/install.doxygen b/.travis/install.doxygen
index 79b0ab2d8e2ba43038ebad9633d0323cb4a367aa..7a425f33da380f8acd1753b03fd8c83794d3e4a4 100755
--- a/.travis/install.doxygen
+++ b/.travis/install.doxygen
@@ -17,8 +17,11 @@ fi
 
 git checkout $version
 
-./configure --prefix="$HOME/opt"
-make
+mkdir build
+cd build
+cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$HOME/opt" ../
+make -j 4
 make install
+
 cd ../