diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt
index 92ae62c2c48a564b4648a14e83c561ee000d1a3d..fccf49a1f678923ac3895f8653031cdf04f7927e 100644
--- a/user-doc/Installation.txt
+++ b/user-doc/Installation.txt
@@ -394,6 +394,9 @@ variable when installing, PLUMED will be installed in /usr/local.
 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`.