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Removed duplicate doc files #270

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merged 7 commits into from
Oct 9, 2019
Merged

Removed duplicate doc files #270

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a1d0314
temporary fix for dihedrals in CG forcefield
uppittu11 Feb 20, 2019
32e591b
merging with mosdef-hub/foyer
uppittu11 Sep 20, 2019
61523c2
Merged with upstream/master
uppittu11 Oct 1, 2019
5817af2
added color to code, fixed embedded hyperlink
uppittu11 Oct 7, 2019
721a773
removed forcefields.rst (duplicate)
uppittu11 Oct 7, 2019
d574fe2
removed auto-generated version.py
uppittu11 Oct 7, 2019
684382c
update 'parameter_definitions' link in index.rst
uppittu11 Oct 7, 2019
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90 changes: 0 additions & 90 deletions docs/forcefields.rst
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2 changes: 1 addition & 1 deletion docs/index.rst
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Expand Up @@ -77,7 +77,7 @@ views of the National Science Foundation.
.. toctree::
:hidden:

forcefields
parameter_definitions

.. toctree::
:hidden:
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7 changes: 4 additions & 3 deletions docs/parameter_definitions.rst
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Expand Up @@ -37,8 +37,9 @@ Definitions for each molecular force follow the OpenMM standard.
Classes vs. Types
-----------------

OpenMM allows users to specify either a ```class`` or a
``type`` <http://docs.openmm.org/7.0.0/userguide/application.html#atom-types-and-atom-classes>`__,
OpenMM allows users to specify either a ``class`` or a
``type`` (See `Atom Types and Atom Classes
<http://docs.openmm.org/7.0.0/userguide/application.html#atom-types-and-atom-classes>`_),
to define each particle within the force definition. Here, ``type``
refers to a specific atom type (as defined in the ``<AtomTypes>``
section), while ``class`` refers to a more general description that can
Expand All @@ -60,7 +61,7 @@ considered to be more specific.

**Example:**

::
.. code:: xml

<RBTorsionForce>
<Proper class1="CT" class2="CT" class3="CT" class4="CT" c0="2.9288" c1="-1.4644" c2="0.2092" c3="-1.6736" c4="0.0" c5="0.0"/>
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