GitLab

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