Updated the default water to SSD/E
backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc
formatting fixes and new atypes in LJFF
fixed a few references to older stuff...
Changes for SSD/E
Switched the bond in the force field back to constrained, to preserve energy
Changed over the bonds to Harmonic bonds in the DUFF frc file
added Harmonic bod into the DUFF forcefield and BondExtensions.cpp
slowly converting to new integrator and forcefield names.
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