Add magic bytes
Update ContextImpl.cpp
Typo fix (represnted -> represented) and remove the execution permission bit
from all .cpp and .h files.
Merge branch 'master' of http://github.com/SimTk/openmm
First pass at adding my CHARMM compatibility layer.

Currently gives exactly the same energy as the same files passed through chamber
(which, in turn, was validated to machine precision against CHARMM itself).
Add new package to setup.py
Import the CHARMM objects into the toplevel namespace of the app layer.
Add base exception classes.
Fix remaining bugs with CHARMM integration.
Add some protection against an uncaught exception in the CharmmFile destructor

Add a test case and example for running with CHARMM files.
Update the simtk/openmm/app/charmm/__init__.py file with the MIT license and
correct list of modules (the existing list was for the ParmEd implementation
which separated out the OpenMM integration so not having it was not fatal).
Merge branch 'master' of http://github.com/SimTk/openmm
Add a couple unittests for CHARMM files.  Good thing, too, because they helped
pick up some bugs that were not caught in my initial test following the port
from ParmEd.

All 4 tests pass right now, although no periodic systems are being tested.
Currently CHARMM, XPLOR, and VMD tests are all being run (for the same ala-3
system).

Disable implicit solvent tests, since there is no robust radii assignment
routine yet (the radii are stored in the Amber topology file).  I will port my
assignment routine from ParmEd here shortly and then re-enable the GB tests.
Clarify a docstring.
Add support for the Amber GB forces.  Put in the correct radii determination
(again, code pulled from ParmEd) and update the tests to include this.
Move charmm package to internal.
Add the PSF files and CHARMM 22 files to the install lists (I think?? I've never
really used CMake in-depth before).

Hopefully this fixes the Travis-CI build failures.
Add a positions setter and improve the error message when someone fails to load
parameters to a ProteinStructure before calling createSystem.
Merge branch 'master' of http://github.com/SimTk/openmm
First pass at making a consistent API.