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Python records where OpenMM is installed, so it doesn't need to be specified with environment variables at runtime

Lots of code cleanup related to constraints in the reference platform

Added option to omit PILE thermostat from RPMD

Created reference implementation of SETTLE

Python records where OpenMM is installed, so it doesn't need to be specified with environment variables at runtime

dmstests

Fix to PR #152

Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular import and 1 bugfix where dms wasn't creating the topology correctly when the water was specified in different chains

Ignore constraints that connect two massless particles (feature request 1915)

Create system from Desmond files

add getByAtomicNumber to element.

ATOM lines should be 80 chars

Fix bug in gromacs top file parser

Look for gromacs include directory in a more flexible way