diff --git a/CHANGES/v2.0.txt b/CHANGES/v2.0.md
similarity index 99%
rename from CHANGES/v2.0.txt
rename to CHANGES/v2.0.md
index 659a47c2109e5f984b7db56f994e658e8e82265e..e5b6f0204dfded0f7bca61236c94cd851acb25a7 100644
--- a/CHANGES/v2.0.txt
+++ b/CHANGES/v2.0.md
@@ -1,5 +1,3 @@
-/**
-
 @page CHANGES-2-0 Version 2.0
 
 Version 2.0.0 (Sep 27, 2013)
@@ -163,9 +161,3 @@ For developers:
 - Added warning when performing regtests using an instance of plumed from
   a different directory
 
-
-*/
-
-
-
-
diff --git a/CHANGES/v2.1.txt b/CHANGES/v2.1.md
similarity index 99%
rename from CHANGES/v2.1.txt
rename to CHANGES/v2.1.md
index 320e3745f6745632e1bbdef8b0c67d6357445898..d42aba60bd4432964f9f661b5470a64192abbc9c 100644
--- a/CHANGES/v2.1.txt
+++ b/CHANGES/v2.1.md
@@ -1,5 +1,3 @@
-/**
-
 @page CHANGES-2-1 Version 2.1
 
 Version 2.1.0 (Sep 15, 2014)
@@ -250,6 +248,3 @@ For users:
 - PLUMED now reports an error when using \ref HISTOGRAM with FREE-ENERGY without USE_ALL_DATA. See \issue{175}
 - Fixed a bug in configure together with --enable-almost. The check for lbz2 library was not working properly.
 
-
-
-*/
diff --git a/CHANGES/v2.2.txt b/CHANGES/v2.2.md
similarity index 99%
rename from CHANGES/v2.2.txt
rename to CHANGES/v2.2.md
index 5009958451bfc1d9cf8c4ac9488bac27aa193f5e..d6843f79364de090de660946c13a15723129c3fd 100644
--- a/CHANGES/v2.2.txt
+++ b/CHANGES/v2.2.md
@@ -1,5 +1,3 @@
-/**
-
 @page CHANGES-2-2 Version 2.2
 
 Version 2.2 (Oct 13, 2015)
@@ -194,4 +192,3 @@ For users:
 - Added an automatic flush of HILLS files when using \ref METAD with file-based multiple walkers.
 - Root dir is logged to allow easier debugging of problems.
 
-*/
diff --git a/CHANGES/v2.3.txt b/CHANGES/v2.3.md
similarity index 99%
rename from CHANGES/v2.3.txt
rename to CHANGES/v2.3.md
index 287903c8c503e01130b534a96a5a76cd778a1ffd..45075319cf2b1da0c1bc3ec395d66fd1b3122b2a 100644
--- a/CHANGES/v2.3.txt
+++ b/CHANGES/v2.3.md
@@ -1,5 +1,3 @@
-/**
-
 @page CHANGES-2-3 Version 2.3
 
 Version 2.3 (Dec 12, 2016)
@@ -188,4 +186,3 @@ For developers:
 - On travis-ci, docs for unofficial or unsupported branches are set not to be indexed by search engines (see \issue{239})
 - Cppcheck on travis-ci has been updated to 1.79.
 
-*/
diff --git a/CHANGES/v2.4.txt b/CHANGES/v2.4.md
similarity index 99%
rename from CHANGES/v2.4.txt
rename to CHANGES/v2.4.md
index 86070c714599e6eb20c58a92c9ac525a16726cb1..61b3b0095f051c46e99b0da921401f95689b703e 100644
--- a/CHANGES/v2.4.txt
+++ b/CHANGES/v2.4.md
@@ -1,5 +1,3 @@
-/**
-
 @page CHANGES-2-4 Version 2.4
 
 Version 2.4 (coming soon)
@@ -82,4 +80,3 @@ Changes from version 2.3 which are relevant for developers:
   - Fixed a potential bug using single precision system blas on a mac (notice that currently plumed only uses
     double precision, so it is harmless).
   - Added `--enable-rpath` option for autoconf (off by default).
-*/
diff --git a/CHANGES/v2.5.txt b/CHANGES/v2.5.md
similarity index 92%
rename from CHANGES/v2.5.txt
rename to CHANGES/v2.5.md
index c02bdd7d0eff8e616ac0526d55d73cad052162bd..dbbed1220c19fa592c036be91508ce3d6b8ead32 100644
--- a/CHANGES/v2.5.txt
+++ b/CHANGES/v2.5.md
@@ -1,7 +1,4 @@
-/**
-
 @page CHANGES-UNRELEASED Unreleased changes
 
 This page contains changes that will end up in 2.5
 
-*/
diff --git a/release.sh b/release.sh
index 83fceaaa777b2c28341304b0b72e282633fb6473..1d7293cd4ff8a6058b8c3479a4c9d56074a8c803 100755
--- a/release.sh
+++ b/release.sh
@@ -111,7 +111,7 @@ git checkout v$shortversion
 
 set -e
 if ! test "$VALIDATED" ; then
-  update_changelog CHANGES/v$shortversion.txt $version $shortversion "coming soon"
+  update_changelog CHANGES/v$shortversion.md $version $shortversion "coming soon"
   echo 
   msg="Travis tests for v$version
 
@@ -119,12 +119,12 @@ if ! test "$VALIDATED" ; then
   echo "Now I will add an empty commit and push the result to origin"
   echo "I will use the following commands:"
   echo "***"
-  echo "git add CHANGES/v$shortversion.txt"
+  echo "git add CHANGES/v$shortversion.md"
   echo "git commit --allow-empty -m \"$msg\""
   echo "git push origin v$shortversion"
   echo "***"
   confirm || exit
-  git add CHANGES/v$shortversion.txt
+  git add CHANGES/v$shortversion.md
   git commit --allow-empty -m "$msg"
   git push origin v$shortversion
   echo
@@ -136,7 +136,7 @@ if ! test "$VALIDATED" ; then
   echo "  http://plumed.github.io/doc-v$shortversion"
   echo "In case of success, relaunch this script as \"./release.sh --validated\""
 else
-  update_changelog CHANGES/v$shortversion.txt $version $shortversion "$(date '+%b %e, %Y' | sed 's/  / /g')"
+  update_changelog CHANGES/v$shortversion.md $version $shortversion "$(date '+%b %e, %Y' | sed 's/  / /g')"
   {
     grep  \# VERSION 
     echo $version
@@ -153,7 +153,7 @@ else
   echo "push it to origin and create a tgz file"
   echo "I will use the following commands:"
   echo "***"
-  echo "git add CHANGES/v$shortversion.txt"
+  echo "git add CHANGES/v$shortversion.md"
   echo "git add VERSION"
   echo "git commit --allow-empty -m \"$msg\""
   echo "git tag v$version"
@@ -161,7 +161,7 @@ else
   echo "git archive -o plumed-$version.tgz --prefix plumed-$version/ v$version"
   echo "***"
   confirm || exit
-  git add CHANGES/v$shortversion.txt
+  git add CHANGES/v$shortversion.md
   git add VERSION
   git commit --allow-empty -m "$msg"
   git tag v$version
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 7a884face6c60aff15d88b8b1b61eb0a5e1a50cc..0242c88cbdb0e7e34116479318e4da270c0c4a66 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -784,7 +784,7 @@ INPUT_ENCODING         = UTF-8
 # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf,
 # *.qsf, *.as and *.js.
 
-FILE_PATTERNS          = *.txt
+FILE_PATTERNS          = *.txt *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.