Updated manual, and altered some language in the force field files
Fixed a force field atom problem
Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
Fixed some broken comments for use with Doxygen. Made changes to allow topology-based force-field overrides in include files. Fixed a calculation of box quadrupole moments for molecules with point dipoles.
Latest
Fixed a few DumpWriter / FlucQ bugs. Still working on Ewald, updated Quadrupolar test structures.
MERGE OpenMD development branch 1465:1781 into trunk
Modified lines for new GayBerneAtomTypes section parser
Adding Repulsive Power potential
Added the EADM.frc forcefield file -JRM
This commit should allow EADM simulations to be run on the cluster. Main additions include EADM_FF.hpp/cpp as well as a system dipole correlation option in DynamicProps.
Matched default Charges for OH and HO (Hydroxyl) to the values from OPLS paper.
Changed DUFF to match new option section format.
Completed SMIPD to Langevin Hull integrator name change
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