diff --git a/doc/lammps.1 b/doc/lammps.1
index c10950643d..11438ac5c3 100644
--- a/doc/lammps.1
+++ b/doc/lammps.1
@@ -1,4 +1,4 @@
-.TH LAMMPS "8 April 2021" "2021-04-08"
+.TH LAMMPS "14 May 2021" "2021-05-14"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst
index 9198f545bc..4c7e5fa8f5 100644
--- a/doc/src/Manual.rst
+++ b/doc/src/Manual.rst
@@ -89,10 +89,15 @@ Programmer Guide
    Modify
    Developer
 
+*****************
+Command Reference
+*****************
+
+.. _command_reference:
 .. toctree::
-   :caption: Index
-   :name: index
-   :hidden:
+   :name: reference
+   :maxdepth: 1
+   :caption: Command Reference
 
    commands_list
    fixes
@@ -118,7 +123,7 @@ Indices and tables
 .. admonition:: Web Browser Compatibility
 
    The HTML version of the manual makes use of advanced features present
-   int "modern" web browsers.  This can lead to incompatibilities with older
+   in "modern" web browsers.  This can lead to incompatibilities with older
    web browsers (released more than 4 years ago) and specific vendor browsers
    (e.g. Internet Explorer on Windows; Microsoft Edge works well though)
    where parts of the pages are not rendered as expected (e.g. the layout is
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index 41c9732c62..d54594d5af 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -244,6 +244,7 @@ accelerated styles exist.
 * :doc:`lb/viscous <fix_lb_viscous>` -
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
+* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst
index a2f25780f5..76506f3e19 100644
--- a/doc/src/fix_mdi_engine.rst
+++ b/doc/src/fix_mdi_engine.rst
@@ -1,4 +1,4 @@
-.. index:: fix move
+.. index:: fix mdi/engine
 
 fix mdi/engine command
 ======================
diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst
index 927a518f4e..b39999606d 100644
--- a/doc/src/mdi_engine.rst
+++ b/doc/src/mdi_engine.rst
@@ -1,4 +1,4 @@
-.. index:: mdi_engine
+.. index:: mdi/engine
 
 mdi_engine command
 ==================
diff --git a/doc/utils/sphinx-config/_static/css/lammps.css b/doc/utils/sphinx-config/_static/css/lammps.css
index b69405365a..900054eeeb 100644
--- a/doc/utils/sphinx-config/_static/css/lammps.css
+++ b/doc/utils/sphinx-config/_static/css/lammps.css
@@ -35,6 +35,10 @@ hr {
      display: none;
 }
 
+#command-reference.section h2 {
+     display: none;
+}
+
 .ui.tabular.menu .item {
     padding-right: 1em;
     padding-left: 1em;
diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in
index 17cb3c2395..baf472b9f9 100644
--- a/doc/utils/sphinx-config/conf.py.in
+++ b/doc/utils/sphinx-config/conf.py.in
@@ -241,7 +241,7 @@ html_show_sourcelink = False
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'LAMMPSdoc'
 
-html_add_permalinks = ''
+html_permalinks = True
 
 if 'epub' in sys.argv:
   html_math_renderer = 'imgmath'
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 7bbafaeafb..6133729b8a 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -2850,6 +2850,8 @@ Runge
 runtime
 Rutuparna
 rx
+rxnave
+rxnsum
 ry
 rz
 Ryckaert
diff --git a/src/version.h b/src/version.h
index d7839fcbfe..39344fdf55 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "8 Apr 2021"
+#define LAMMPS_VERSION "14 May 2021"