Merge pull request #5030 from epretti/cleanup-examples

Cleanup examples, documentation, and README files

examples/extras/README.md

-OpenMM extra utility scripts
-============================
+## OpenMM extra utility scripts
 
 This directory contains standalone utility scripts for use with OpenMM.
 

examples/python-examples/CMakeLists.txt

+# Install Python examples.
+
+INSTALL(FILES simulateAmber.py input.inpcrd input.prmtop DESTINATION examples/python-examples)
+INSTALL(FILES simulateCharmm.py ala_ala_ala.pdb ala_ala_ala.psf charmm22.par charmm22.rtf DESTINATION examples/python-examples)
+INSTALL(FILES simulateGromacs.py input.gro input.top DESTINATION examples/python-examples)
+INSTALL(FILES simulatePdb.py input.pdb DESTINATION examples/python-examples)
+INSTALL(FILES argon-chemical-potential.py DESTINATION examples/python-examples)

examples/argon-chemical-potential.py → examples/python-examples/argon-chemical-potential.py

@@ -7,8 +7,8 @@
 #
 # REQUIREMENTS
 #
-# numpy - Scientific computing package - http://numpy.scipy.org
-# pymbar - Python implementation of MBAR - https://simtk.org/home/pymbar
+# numpy - Scientific computing package - https://numpy.org/
+# pymbar - Python implementation of MBAR - https://github.com/choderalab/pymbar
 #
 # REFERENCES
 #

platforms/opencl/src/OpenCLPlatform.cpp

@@ -141,7 +141,7 @@ bool OpenCLPlatform::isPlatformSupported() {
     if (major < 14 || (major == 14 && minor < 3))
         // 14.3.0 is the darwin release corresponding to OS X 10.10.3. Versions prior to that
         // contained a number of serious bugs in the Apple OpenCL libraries.
-        // (See https://github.com/SimTk/openmm/issues/395 for example.)
+        // (See https://github.com/openmm/openmm/issues/395 for example.)
         return false;
 #endif
 

wrappers/python/openmm/unit/mymatrix.py

 """
-Pure python inversion of small matrices, to avoid requiring numpy or similar in SimTK.
+Pure python inversion of small matrices, to avoid requiring numpy or similar in OpenMM.
 
 This is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of