Fix to the issue #338 and issue #335

[msoroush]

Fix the error in calculating intra-nonbonded energies for polar system, where rCutCoulomb is different from rCut. Now we only Use the LJ cutoff (rCut) do calculate the intra-nonbonded energies.
Increase the tolerance to 10 degree. If sum Angles +/- 10 was close to 360, we keep the angles rigid for cyclic molecules.

[GregorySchwing]

Should we be concerned with electrostatic cutoffs for intra-terms? The inter terms have an overlap array which checks

if(forcefield.rCutLowSq < distSq) and the CalcCoulomb method checks if**(distSq < forcefield.rCutCoulombSq)**

But, there is no equivalent for intra terms. The CalcCoulombAdd_1_4, and CalcCoulombAdd_1_3 methods should have
if(forcefield.rCutCoulombSq[b] < distSq)
return 0.0;

Also, we don't check for if(forcefield.rCutLowSq < distSq) for intra-interactions, which seems like it could occur.

What is the reason for this?

[msoroush]

Should we be concerned with electrostatic cutoffs for intra-terms? The inter terms have an overlap array which checks

if(forcefield.rCutLowSq < distSq) and the CalcCoulomb method checks if**(distSq < forcefield.rCutCoulombSq)** But, there is no equivalent for intra terms.

We check forcefield.rCutLowSq < distSq to reject the move that causes overlap between atoms, this overlap only needs to be check for inter energy, not intra energy. When only need to calculate inter-nonbonded coulomb if they are within forcefield.rCutCoulombSq. This is because of ewald summation method. For intra-nonbonded coulomb, we dont use ewlad, so no need to compare with forcefield.rCutCoulombSq.

The CalcCoulombAdd_1_4, and CalcCoulombAdd_1_3 methods should have
if(forcefield.rCutCoulombSq[b] < distSq)
return 0.0;

@jpotoff correct me if I am wrong, but for calculating intra-nonbonded energy, I am using only one cutoff value rCut. The issue was inconsistency in using cutoff when we calculate intra-nonbonded energy in startup (uses rCut) and CBMC (uses max (rCut, rCutCoulomb)). In this pull request, we are only using rCut everywhere in code, to calculate intra-nonbonded energy.
@GregorySchwing similar to CalcAdd_1_4, no need to check the distance.

Also, we don't check for if(forcefield.rCutLowSq < distSq) for intra-interactions, which seems like it could occur.

We dont check for overlap, when we calculate intra-nonbonded energy, only in inter-nonbonded energy.

[msoroush]

@GregorySchwing Can you review the latest change in this Pull request?