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TestAmberPrmtopFile.py tests take 17 seconds combined on my laptop).

force field utilizes nbfix functionality. Without this commit, using a ff14IPQ
topology file (or one modified by ParmEd to contain off-diagonal LJ elements),
would happily run, but ignore off-diagonal elements.

The new Chen and Garcia RNA force field (see doi:10.1073/pnas.1309392110) also
utilizes off-diagonal terms in its parametrization scheme.

One shortcoming is that the approach taken here -- using a pair parameter lookup
table -- cannot be currently used with a long-range correction because it is not
a `Continuous1DFunction' by virtue of using two `Discrete2DFunction'
TabulatedFunction classes.

Energies here match the values obtained with Amber to 0.01 -- 0.1 kcal/mol
(within 0.1% of the total).

itself. This way each parm is only read once for every test (rather than being
read for every test, even when they're not used, as part of the setUp routine).
For large systems, this makes the tests run a lot faster (for small systems it's
not a large speedup).

All tests continue to pass. This change also tests that the various calls to
createSystem and such do not actually change the object in a detrimental way.

the switchDistance argument to CharmmPsfFile.createSystem().

Also add a check to protect against negative switching distances.

    - Adjust CharmmPsfFile parser to accept multiple blank lines before the
      NATOM record (I saw 1 PSF file like this... not sure how common it really
      is)
    - Removed the shebang line from element.py and removed execute permissions--
      it should never be executed directly (evidenced by the fact that the
      original shebang line was wrong and would never work, anyway).
    - Fix a test to determine if a Bond is part of an Angle in the PSF data
      structures.

(which means that consecutive residues may have the same residue number _and_
name, but are different residues).

former has a single entry for all unique dihedrals. The latter has a separate
entry for every _term_ of every dihedral (and the latter is the one with the
parameters loaded into it). This way, parameter sets can be reloaded at will
without relying on the hack that createSystem previously employed (i.e., backing
up the dihedral array, clobbering it, then putting it back). This way is cleaner
and safer (although functionally equivalent for typical OpenMM use).

boxVectors, so they should be a property computed from the vectors). Also make
sure that any attempts to change the boxVectors correspondingly deletes the
cached copies of the box lengths so they are recomputed if necessary.

different from _all_ of the others.

element.

fix the remaining CI issues.

Also make sure .ncrst files are copied over in the test directory.