removing spurious cutoffGroup lines from default water.md sample files

adding interface

Adding one RNEMD sample

Adding samples for SMIPD.

Added large quantities of code for convex hull and constant pressure langevin dynamics.

Code work on thiols and TraPPE torsions.

Added model for thiols.

Changes....

Added more surfaces.

Many fixes for Charmm-type torsions.

Broken files on install

fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1

Adding a starter file for the secondary prism {1,1,-2,0} face.

new ideal structures

more openbabel updates, also changing velocitizer to thermalizer to
avoid a filename collision on case-insensitve file systems

Adding samples for builders

fixing missing lattice arguments, adding a builder sample

Fixing the builders to prepare for OOPSE-4 release

Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.

Added tred to sample water.md files

added mpi compilers, demoted pg compilers after pathscale

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

Adding single precision capabilities to c++ side

Removed sqrt splines and shape stuff (doesn't work, so why was it in there?).  Changed some of the water samples to use shifted_force.  Probably should set the defaults to use the damped version now that we sped it up.

splined up sticky

Many performance improvements

Changes to cutoff radius setting to a more logical procedure - still may change...

Missing Makefile in this sample directory

unifying function name in electrostatics

Sutton and Chen should be working now.

More Sutton-Chen bug fixes.

added files for sutton-chen

More moving...

More Directory changes...

Removed one parasitic argon atom which was living inside the GB
particle.  No alien-like ripping out of the stomach was required.

removing deprecated nAtoms and nComponents lines

just some parameters

just playing around - we need to refresh all the samples sometime soon...

playing with switching functions

mmm...  damped shifted force...

minor changes when testing reaction field

nothing

added a few GB test cases

Adding .md files for GB/LJ tests

Adding some cutoff tests

Testing new cutoff methods

just some random changes when testing

fixing up some samples

fixed up some sample md files

reaction field seems to work now, still need to do some testing...

Equilibrated the sample

fixed a bug and ran a simulation

Included a tap dimer for testing purposes

Modifications to tap.  Also correcting changes to the previous merge that were not caught

Changed SHED to TAP

Added TIP4P-Ew

Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...

some samples are not installed correctly

added quadrupole sample

messing with samples

changes during debug of charge-dipole

added some samples

messing with the split dipole test cases

Oops...  MPI now builds...

fixes to restraints

First commit of the new restraints code

making some cool test cases

fixed a sample

Back to normal... Oh... Restraints should work in parallel now

working sample

testing force fields

shorter run

uncommented .in line

fix Makefile under water directory

Remove some Makefile.in

Import of OOPSE v. 2.0