GitLab

Fixed errors in LJ interactions with CHARMM36

Fixes to CHARMM36 force field

allow the user to skip parameter condensing CHARMM parameters

Added link to openmm-forcefields in the manual

Updated CUDA version in prepare script

Avoid truncating PDB file if the IDs are too long

Improved documentation on how to set parameters

Documentation updates for 7.2

Fix Quantity.__setitem__ bug with slice assignment

Fix Bond pickling in Python 2.7

Eliminate stray non-ASCII characters from references.bib since this breaks sphinx

The pickle round trip for the Bond object does not preserve the `type` and `order` parameters in Python 2.7.

Near as I can tell, its because the parent `namedtuple` already has a __getstate__ method, so the default
of returning the `__dict__` is never given, so `__setstate__` is not called (as default). This leads to pickle
 restoring the state, but never invoking the `__new__` statement, resulting in `type` and `order` being
 lost.

 This PR fixes this problem in python 2.7, without breaking python 3.x versions.

 Related mdtraj/mdtraj#1308

Can build arbitrary membranes by supplying a pre-equilibrated patch

Updated reference for ipq force field

Created membrane builder

Added new Amber and CHARMM force fields

Improvement to processing of includes in force fields

Optimized creation of proper torsions