Allow for certain angle types to use 1-3 nonbonded interactions instead of harmonic angles

[cwalker7]

It seems that the energy spiking issue #86 may be due to an issue with the angle/torsion nonbonded exclusions. It seems that some nonbonded interactions are not being enforced. For a single Langevin dynamics simulation at 400K with LJ epsilon=5kJ/mol, and bond angle potentials turned on, a pairwise rdf distribution for backbone-sidechain distances shows that bb and sc beads are frequently right on top of eachother. Naturally, this makes the system very unstable.

Torsions with a force constant of 0 should be ok, provided that the 1-4 nonbond scaling is set 1 (which it is currently unless we are considering rosetta exceptions).

We should allow for certain angle types to keep their 1-3 nonbonded interactions, rather than setting a default force constant which is applied to all angles. Or in the short term, make sure that a force constant of zero is not allowed.

However I think the spiking issue is more than this - here's what we see for different variations:

• include_bond_angle_forces=False, include_torsion_forces=False --> no spiking
• include_bond_angle_forces=True, all k_angle are 25 kJ/mol/rad^2, include_torsion_forces=True --> spiking
• include_bond_angle_forces=True, all k_angle are 25 kJ/mol/rad^2, include_torsion_forces=False --> spiking
• include_bond_angle_forces=False, include_torsion_forces=True --> spiking