OpenMD

Aluminum fixes

Added EAM line for Art Voter's aluminum potential

new params

Added some missing bend and torsion types

Install bugs, tweaks of samples

fixing make install process

Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

Adding alternate water models to Amber parameters.  The approved model
for Amber is still TIP3P, but if you want reasonable water dynamics,
you need SPC/E.  OOPSE/OpenMD will now give you the choice.

fixed a few bugs in the options, added base atom types

Fixes for Torsions and Inversions, Amber is mostly working now.

All Your Base are belong to us!

fixed some incorrect types

Changed parameters for S-S interactions on gold surface.

Changes to thiol model.

Adding infrastructure for Amber force field

Added TraPPE torsions for thiols.

Adding Trappe torsion types and fixing Opls types

Code work on thiols and TraPPE torsions.

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Changes.

Removed accidental print lines.

Fixed typo in LJinteraction types. LJ-metal appears to work now.

Added parameters for Lennard-Jones Thiol potential.

Checking in changes for Hefland moment calculations

Changes....

Changes to MAW. New form of the potential and cleanup.

Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

Added metal-non-metal section

Broken files on install

Added MnM forcefield.

Changes to sutton-chen force.

updated OpenBabel to version 2.0.2

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 parameters to forcefield

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

Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)

added DPD molecule type parameters

Changes in Sutton-Chen units

All of the OpenBabel stuff needs to be installed

Changed conversion factor.

Added energy scaling to section parsers.

Add force file.

Changes in forcefield.

Adding .frc file for CLAYFF

adding openbabel data files

Added sutton-chen to makefile.

Added force files for Sutton-Chen and Quantum Sutton-Chen

added a test atom type

Fixing GB parameters

Changed the parameters for the Gay-Berne type

Add parts for the GayBerne LJ

Messing with 2-point water models

Added DIP atom types for 2-point water model

re-added Cl- and Na+

Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month...

just some tap changes

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

added gb

Better tap

Couple of changes for TAP water.  Need to parametrize.

Changed SHED to TAP

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

Added TIP4P-Ew

fixing of the quadrupoles

added Cl- and Na+

Corrected changes to the forcefield files

Chris debugging stuff.  HE WILL CHANGE THIS BACK, RIGHT?

quadrupoles for SSD models

minor change

fix a bug in SectionParser (lineNo is not updated)

change the format of DUFF2

Added a charge for Chlorine

forget to set dipole for lipid head group

sync Makefile

remove some useless force fields

adding new format of EAM force field

rename newDUFF.frc to DUFF2.frc

adding new EAM force field files

merge WATER force field into DUFF

change the force constant of bonds

minor fix in DUFF

minor fix in force field file

minor fix

new ForceField format

new DUFF forcefield

adding new format DUFF force field

add Makefile

Import of OOPSE v. 2.0