License and links update

README.md

@@ -6,13 +6,13 @@
 
 ### Introduction
 
-[OpenMM](http://openmm.org) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
+[OpenMM](https://openmm.org) is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
 provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.  
 
 ### Getting Help
 
 Need help using OpenMM?  There are several places that you can find it:
-- [Documentation](http://docs.openmm.org/):
+- [Documentation](https://docs.openmm.org/):
   - [User Manual](https://docs.openmm.org/latest/userguide/)
   - [Python API Reference](https://docs.openmm.org/latest/api-python/)
   - [C++ API Reference](https://docs.openmm.org/latest/api-c++/)

SUPPORT.md

@@ -10,5 +10,5 @@ you want to suggest a change to the code, or if you think you have found a bug,
 open an issue.  The core developers monitor both, so don't worry if you aren't
 sure which one is most appropriate for your question.  We will see it either way.
 
-You also may want to consult the [documentation](http://docs.openmm.org/).  It is quite
+You also may want to consult the [documentation](https://docs.openmm.org/).  It is quite
 thorough, and you may be able to find the answer to your question.

docs-source/developerguide/license.rst

+License
+*******
+
 Portions copyright (c) 2011-2025 Stanford University and the Authors
 
 Contributors: Peter Eastman
@@ -21,9 +24,8 @@ OUT OF OR IN CONNECTION WITH THE DOCUMENT OR THE USE OR OTHER DEALINGS IN THE
 DOCUMENT.
 
 Acknowledgments
+***************
 
-OpenMM software and all related activities, such as this manual, are funded by
-the Simbios National Center for Biomedical Computing through the National
-Institutes of Health Roadmap for Medical Research, Grant U54 GM072970.
-Information on the National Centers can be found at
+OpenMM research and development activities are supported by various individuals
+and funded from a number of sources: for up-to-date information, consult
+https://openmm.org/development.
\ No newline at end of file
-https://commonfund.nih.gov/bioinformatics.

docs-source/usersguide/introduction.rst

@@ -25,8 +25,11 @@ Online Resources
 ****************
 
 You can find more documentation and other material at our website
-http://openmm.org.   Among other things there is a discussion forum,
-a wiki, and videos of lectures on using OpenMM.
+https://openmm.org/.  In particular, you may want to consult the
+`Python API documentation <https://docs.openmm.org/latest/api-python/>`__ or the
+`C++ API documentation <https://docs.openmm.org/latest/api-c++/>`__, read the
+`Frequently Asked Questions (FAQ) <https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions>`__,
+or browse the `discussion forum on GitHub <https://github.com/openmm/openmm/discussions>`__.
 
 
 Referencing OpenMM
@@ -48,8 +51,6 @@ citations of our publication will help demonstrate the value of OpenMM.
 Acknowledgments
 ***************
 
-OpenMM software and all related activities, such as this manual, are funded by
-the Simbios National Center for Biomedical Computing through the National
-Institutes of Health Roadmap for Medical Research, Grant U54 GM072970, and by
-National Institutes of Health grant R01-GM062868.
-
+OpenMM research and development activities are supported by various individuals
+and funded from a number of sources: for up-to-date information, consult
+https://openmm.org/development.

docs-source/usersguide/library/03_tutorials.rst

@@ -9,8 +9,8 @@ the OpenMM C++ API (as well as the C and Fortran API wrappers).
 Example Files Overview
 **********************
 
-Four example files are provided in the examples folder, each designed with
-a specific objective.
+Four example files are provided in the :code:`examples/cpp-examples` folder,
+each designed with a specific objective.
 
 * **HelloArgon:**  A very simple example intended for verifying that you
   have installed OpenMM correctly.  It also introduces you to the basic classes
@@ -248,7 +248,7 @@ and C examples.
 The Fortran compiler needs to load a version of the libstdc++.dylib library that
 is compatible with the version of gcc used to build OpenMM;   OpenMM for Mac is
 compiled using gcc 4.2.  If you are compiling with a different version, edit the
-Makefile and add the following flag to FCPPLIBS: :code:`–L/usr/lib/gcc/i686
+Makefile and add the following flag to FCPPLIBS: :code:`-L/usr/lib/gcc/i686
 -apple-darwin10/4.2.1`\ .
 
 When the Makefile has been updated, type:

docs-source/usersguide/license.rst

+License
+*******
+
 Portions copyright (c) 2008-2025 Stanford University and the Authors
 
 Contributors:  Kyle Beauchamp, Christopher Bruns, John Chodera, Peter Eastman, Mark