RMSD under 1, flatbottom, runs without exploding, global force constant, temp coupling

[jkwoods]

• added slow turn on global force constant - only way to stop explosion (?? at least within my limited knowledge)
• global force constant eliminates the need for -k in the custombondforce for whatever reason
• added a pdbwriter for trajectory/testing purposes - one line, should be easy to delete later
• started incorporating the amber linear peptide stuff and rst builders - currently in progress but doesn't screw up anything else
• added a bunch of testing pdbs/rst/data
• added new thermostat, integrator, flatbottom rst
• added temp coupling collision stuff
• fine-tuned collisions, temperature
• in progress: velocity limit, cuttoffnonperiodic stuff (big proteins don't do well yet)