Merge branch release-2018 into release-2019

[alexxy/gromacs.git] / docs / user-guide / index.rst

diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst
index 5a352a5242173da497eb0b901ba4d9fb0e1d84dc..ad509c9eca0c6fa015c42f549821bc8ea1e8f05c 100644 (file)
--- a/docs/user-guide/index.rst
+++ b/docs/user-guide/index.rst
@@ -1,3 +1,5 @@
+.. _user guide:
+
 **********
 User guide
 **********
@@ -12,9 +14,11 @@ This guide provides
 For getting, building and installing |Gromacs|, see the
 :doc:`/install-guide/index`.
 For background on algorithms and implementations, see the
-`reference manual`_.
+:ref:`reference manual part <gmx-reference-manual-rst>` of the documentation.
+
+|GMX_MANUAL_DOI_STRING|
 
-.. _reference manual: gmx-manual-parent-dir_
+|GMX_SOURCE_DOI_STRING|
 
 .. TODO This is going to require more organization now that
    we are getting more content available.
@@ -33,8 +37,9 @@ For background on algorithms and implementations, see the
    mdrun-features
    mdrun-performance
    run-time-errors
-   file-formats
+   cmdline
    terminology
    environment-variables
    floating-point
    security
+   deprecation-policy