Added nanoBuilder and a general Lattice builder.
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Most of the integrator and NVT seem to be working now.
all seems to be working
fixed up sysBuild to where it should now build our systems
working on the system builder
working on a system builder
added Ghost bends to the TraPPE_Ex forceField added sysBuild to the utils Makefile
Changed Readme, added some files
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