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sqrt of the variance), and average, returning a Quantity with the proper units.

This should be reasonably efficient, as it takes advantage of numpy-accelerated
methods if they're present.

parameter set.

 Changes to be committed:
	modified:   checkpointreporter.py

there is a small typo in checkpointreporter.py in openmm. line 81 has:
self._own_handle = true
instead of True.

terms of supporting PSF files that don't really conform to the "standard" way
that CHARMM prints them.

The downside is that it relies on ! comment tags which I think are comments for
CHARMM.  However, the use of !NATOM and !NBOND and other tags seem to be _much_
more conserved than the general format of the PSF file across different dialects
of PSFs.  So the current approach should be more flexible.

the same format as the rest of the CHARMM stream files I've seen.

simtk.openmm.app namespace to allow users to filter that warning out if they
want to.

single parameter.

- Convert coordinates, velocities, and box vectors into Vec3 objects to avoid a
  subtle bug in the units module with respect to silently modifying mutable
  collections in-place when converting to a new set of units.

Depressing compromise to make the ordering of atoms in improper torsions as consistent as possible with both AMBER and CHARMM

correction by default. Then add a test for using the long-range correction and
_not_ using the long-range correction.  Comment out the test using the
long-range correction since it currently segfaults.  When the fix for the
segfault is added, this test can be reinstated (but the energy has to be
updated)

This change in default makes it consistent with the default behavior for the
classical NonbondedForce, and I would have set that as the default to begin with
if I had known it was supposed to work.

copy-and-paste...

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).

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).