diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index 656f2d90b5023a23aca489be4c2a30f9fed07cb1..ec4ce979518f9b512aec059c677712e61e6138b4 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -59,4 +59,4 @@ Changes from version 2.4 which are relevant for developers:
 - A small number of header files in installed
 - When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearence is the effective one.
 - Internal blas and lapack libraries updated to gromacs 2018.
-
+- Choosing `./configure --prefix=$PWD` does not lead anymore to deletion of all header files.
diff --git a/configure b/configure
index 8023a0533ea4d93fd8d9ea466b143687df52683a..80f30416d152508b79daf90b69335b69fdccaded 100755
--- a/configure
+++ b/configure
@@ -9059,18 +9059,6 @@ fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking If prefix is equal to present working directory" >&5
 $as_echo_n "checking If prefix is equal to present working directory... " >&6; }
 
-# ignore cases where the directory does not exist:
-normalized_prefix="`cd "${prefix}" 2>/dev/null && pwd || true`"
-
-if test "`pwd`" = "$normalized_prefix" ; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-  as_fn_error $? "prefix should not be equal to the present working directory" "$LINENO" 5
-else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
 pkgconfig_bin=""
 
 for ac_prog in pkg-config
diff --git a/configure.ac b/configure.ac
index 1494783c4f2aec683e284950263fbb6dbc3eb195..5f7d1d154fa882e1a2adcd0e30a4db51b5a697af 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1124,16 +1124,6 @@ fi
 
 AC_MSG_CHECKING([If prefix is equal to present working directory])
 
-# ignore cases where the directory does not exist:
-normalized_prefix="`cd "${prefix}" 2>/dev/null && pwd || true`"
-
-if test "`pwd`" = "$normalized_prefix" ; then
-  AC_MSG_RESULT([yes])
-  AC_MSG_ERROR([prefix should not be equal to the present working directory])
-else
-  AC_MSG_RESULT([no])
-fi
-
 pkgconfig_bin=""
 
 AC_PATH_PROGS(pkgconfig_bin,pkg-config)
diff --git a/include/plumed b/include/plumed
deleted file mode 120000
index 5cd551cf2693e4b4f65d7954ec621454c2b20326..0000000000000000000000000000000000000000
--- a/include/plumed
+++ /dev/null
@@ -1 +0,0 @@
-../src
\ No newline at end of file
diff --git a/src/config/Config.inc.in b/src/config/Config.inc.in
index aceda6358bca751af34ca4f0b90ebfa557786967..3f2b264c5080c19b16c4996a0369bc5186efcf6a 100644
--- a/src/config/Config.inc.in
+++ b/src/config/Config.inc.in
@@ -60,7 +60,7 @@ std::string getPlumedHtmldir() {
 }
 
 std::string getPlumedIncludedir() {
-  if(!isInstalled()) return getPlumedRoot()+"/include";
+  if(!isInstalled()) return getPlumedRoot()+"/src/include";
   char *env = std::getenv("PLUMED_INCLUDEDIR");
   std::string ss;
   if( env == NULL) {
diff --git a/src/include/plumed b/src/include/plumed
new file mode 120000
index 0000000000000000000000000000000000000000..b870225aa053ea877524b581926b3536a0bd7314
--- /dev/null
+++ b/src/include/plumed
@@ -0,0 +1 @@
+../
\ No newline at end of file
diff --git a/src/lib/Makefile b/src/lib/Makefile
index f3cb4002b4f2bd3a9c79fdf4313336ff69a559fe..0b85e058b3b08b7d12dbf8fb7bfe0dae465d596c 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -426,7 +426,7 @@ ifeq ($(PLUMED_INSTALL),Install)
 else
 	@echo "export PLUMED_IS_INSTALLED=no" >> $@
 	@echo "export PLUMED_ROOT=\"\$${PLUMED_ROOT-$(realpath ../../)}\"" >> $@
-	@echo "export PLUMED_INCLUDEDIR=\"\$${PLUMED_ROOT}/include\"" >> $@
+	@echo "export PLUMED_INCLUDEDIR=\"\$${PLUMED_ROOT}/src/include\"" >> $@
 	@echo "export PLUMED_HTMLDIR=\"\$${PLUMED_ROOT}\"" >> $@
 	@echo "export PLUMED_PROGRAM_NAME=plumed" >> $@
 	@echo "source \"\$$PLUMED_ROOT\"/scripts/$(subst plumed-,,$(@F)).sh" >> $@
diff --git a/user-doc/Installation.md b/user-doc/Installation.md
index f5332309bf4f5c4c69d65edc4afebe5aa53340c5..3795fbd4ef9c4daa6dfc192de941cff9f07ffdd2 100644
--- a/user-doc/Installation.md
+++ b/user-doc/Installation.md
@@ -425,9 +425,6 @@ If you didn't specify the `--prefix` option during configure PLUMED will be inst
 The install command should be executed with root permissions (e.g. "sudo make install")
 if you want to install PLUMED on a system directory.
 
-\warning Please **do not** set prefix to the current directory (`./configure --prefix=$PWD`). PLUMED
-expects the installation directory to be a different one! You might want to use something like `./configure --prefix=$PWD/install` instead.
-
 Notice that upon installation PLUMED might need to relink a library.
 This was always true until version 2.1, but in version 2.2 libraries should
 only be relinked if one changes the install prefix during when typing `make install`.