Merge branch 'master' into update_ug

docs-source/api-python/index.rst

+.. currentmodule:: simtk.openmm.openmm
+
+OpenMM Python API
+=================
+
+The Python API provides information about the classes and methods available in OpenMM for Python developers.
+
+OpenMM consists of two parts. First, there is a set of :ref:`libraries <library>` for performing many types of computations needed for molecular simulations: force evaluation, numerical integration, energy minimization, etc.
+
+Second, there is an :ref:`application layer <app>`, a set of Python libraries providing a high level interface for running simulations. This layer is targeted at computational biologists or other people who want to run simulations, and who may or may not be programmers.
+
+See the user guide for more details.
+
+
+.. toctree::
+   :maxdepth: 2
+
+   app
+   library

openmmapi/src/ContextImpl.cpp

@@ -449,4 +449,5 @@ void ContextImpl::loadCheckpoint(istream& stream) {
         parameters[name] = value;
     }
     updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
+    hasSetPositions = true;
 }