doc: more on installing PLUMED with ALMOST

[makedoc]

user-doc/Installation.txt

@@ -395,7 +395,8 @@ In order to used some of the NMR based collective variables (\ref CS2BACKBONE an
 To do this the free package ALMOST v.2.1 MUST be dowloaded via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
 ALMOST 2.1 can be found in branches/almost-2.1/ and can be compiled:
 
-\warning ALMOST needs SQLITE3, GZIP and BZIP2 installed on your computer.
+\warning ALMOST needs SQLITE3 and  GZIP installed on your computer.
+\warning ALMOST cannot be installed in the same folder of the source code, use --prefix to install it in a different folder
 
 \verbatim
 > ./configure --prefix="wherever you want it" CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" 
@@ -403,6 +404,13 @@ ALMOST 2.1 can be found in branches/almost-2.1/ and can be compiled:
 > make install
 \endverbatim
 
+Sometimes ALMOST can give errors related to the automake tools. To fix them it is often enough to execute
+\verbatim
+> autoreconf -fi
+> automake
+\endverbatim
+and then repeat the configuration and compilation instructions.
+
 PLUMED will not use the RDCs module of ALMOST so you can ignore the warning about LAPACK.
 
 Once ALMOST is installed, PLUMED 2 can then be configured with ALMOST enabled: