Fix segfault when positions are not 3 dimensional.
Merge pull request #82 from rmcgibbo/setLength

Fix segfault when positions are not 3 dimensional.
Cache the PTX files for compiled kernels
Cache filename specifies whether it was compiled in 32 or 64 bit mode
Eliminated some #defines to improve the efficiency of PTX caching
Can set OPENMM_CACHE_DIR to specify where PTX files should be cached
Merge pull request #84 from peastman/cache

Cache the PTX files for compiled kernels
ForceField tries to figure out why no residue matched a template
Handle extra particles correctly when guessing why no template matched a residue.
Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.
Merge pull request #85 from peastman/templates

ForceField tries to figure out why no residue matched a template
create a simtk.openmm.version module that contains the git revision
dont want to double quote
Moved Python app layer tests into the main source tree
Merge pull request #90 from peastman/master

Moved Python app layer tests into the main source tree
Merge pull request #87 from peastman/molecules

Eliminated a potential stack overflow when identifying molecules
Speed optimization to GromacsTopFile
Merge branch 'master' of https://github.com/SimTk/openmm
Merge pull request #92 from peastman/master

Speed optimization to GromacsTopFile
Merge pull request #89 from rmcgibbo/gitversion

create a simtk.openmm.version module that contains the git revision