qmefp tutorial updated

doc/conf.py

@@ -30,12 +30,12 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-#extensions = [
-#    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme',
-#]
 extensions = [
-    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels',
+    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme',
 ]
+#extensions = [
+#    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels',
+#]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/papers.rst

@@ -53,6 +53,7 @@ QM/EFP models
 ML/EFP models
 ^^^^^^^^^^^^^^
 * `ANI/EFP: Modeling Long-Range Interactions in ANI Neural Network with Effective Fragment Potentials <https://doi.org/10.1021/acs.jctc.4c01052>`_
+* `Beyond the cutoff: Hybrid ML/MM electrostatics for neural network potentials <https://pubs.aip.org/aip/jcp/article/164/10/104102/3382612>`_
 
 Macromolecules and flexible fragments
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/tutorials.rst

@@ -6,8 +6,8 @@ Tutorials
 
 .. _non-covalent_calcs:
 
-Performing EFP calculations on a non-covalently bonded system
--------------------------------------------------------------
+EFP calculations for a non-covalent system (molecular clusters, liquids, etc.)
+-----------------------------------------------------------------------------------------
 
 Step 1. Computing EFP parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -31,12 +31,15 @@ Once EFP parameters of all unique fragments are computed, perform the full-syste
 
 .. _covalent_calcs:
 
-Performing EFP calculations in a covalently bound system
------------------------------------------------------------
+EFP calculations for a covalently bound systems (proteins, polymers)
+--------------------------------------------------------------------
 
-* Learn how to prepare a protein system for
-  `EFP protein-ligand calculations <https://github.com/libefp2/BioEFP-tools/tree/main/bioMAKEFP>`_.
-* To setup QM/EFP (excited states!) calculations in a biological system, see :ref:`applied_efp` tutorial.
+Tutorial `EFP protein-ligand calculations <https://github.com/libefp2/BioEFP-tools/tree/main/bioMAKEFP>`_
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Setting up QM/EFP calculations 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+See our new :ref:`applied_efp` tutorial!