Trying to commit again...
Fixed a bug with initialization
Fixed a bug with initialize
Fixed bug in computeKineticEnergy()
Fixed a bug in the linear minimization with PospQ.

It now runs but generates nan for potential and temperature.  Still bugs, but first time it runs without a runtime error.
Fixed bug with the forces, they are stored as long long and not float.

As of now Villin generates 'reasonable' output, although we still need to verify it.
Fixed a bug with kinetic energy
Cuda -> CUDA
New file
Location of lepton changed in new openmm
Changed number of steps to 40
Changed numsteps to 5
Mesing about badly

I spelled messing wrong.
Oh well.

Merge branch 'openmm5#' of https://github.com/movingpictures83/LTMDOpenMM into openmm5#

Conflicts:
	examples/Villin_NLE_2/sim.conf
Header file for kernel
One more include/ folder, include/LTMD/CUDA
Removed random Gauss function.
Alanine input files.
Removed unnused updateState().
Removed debugging printfs...
Removed LOTS of comments!!