GitLab

Virtual sites are never created by the OpenMM system, and their information is
not parsed from the Gromacs topology file. For now just throw an exception
rather than let them run, since TIP4Pew behaves *very* strangely...

Tabulated erfc() to improve accuracy of energies

Fix Gromacs #define replacement and add support for Gromacs 5

Gromacs uses the preprocessor to replace previously #define'd tokens in strings.
This is used, for instance, to override certain parameters without having to
introduce new file types.  This is how Gromacs implemented ff99SB-ILDN (i.e., by
simply replacing the chi torsion for isoleucine, leucine, aspartate, and
asparagine with a define token).  So OpenMM *was* missing some in-line
parameters that were defined.

The immediate consequence I see is that whenever someone tried to run
ff99SB-ILDN with OpenMM, what they were *really* getting was ff99SB. Not sure
where else, if anywhere, this kind of thing was happening.

Switched to a new Windows pthreads library

Conflicts:
	libraries/pthreads/include/pthread.h

Implemented runForClockTime()

Added checkpointing functions to Simulation

Update setup.py

Improved accuracy of correction for exclusions with PME

mingw has STRUCT_TIMESPEC

Implemented select() in custom expressions

fix mingw build

Fixed failing test cases.  Increased default minimizer tolerance to 10.

Added option to add a fixed number of solvent molecules

fix swig build

Better error catch for using chamber prmtops

Prints out a more helpful error message than a weird regex-based missing
"groups" attribute on NoneType.

Optimization for AMD

CPU PME plugin respects OPENMM_CPU_THREADS environment variable