Write CONECT records to PDB files
Prevent segfaults when a simulation blows up
Merge pull request #170 from peastman/master

Prevent segfaults when a simulation blows up
Take the 1-4 non-bonded scaling parameters from the Amber topology files if
present, defaulting to 1.2 (SCEE) and 2.0 (SCNB) if they're not present. If
values for scee and scnb are provided to readAmberSystem they will override any
values in the topology file, but a warning will be printed (since ignoring the
scaling parameters in the topology file really changes the force field).
Merge pull request #169 from peastman/connect

Write CONECT records to PDB files
Merge pull request #171 from swails/master

Take 1-4 nonbonded scaling parameters from the amber topology file
Lots of optimizations to Lepton, including creating CompiledExpression class.
Converted lots of ExpressionPrograms to CompiledExpressions
Merge pull request #173 from peastman/master

Performance improvements to CPU implementation of custom forces
Updated documentation for Lepton
Merge pull request #174 from peastman/master

Updated documentation for Lepton
Fixed segfaults on some computers
Merge branch 'master' of https://github.com/SimTk/openmm
Merge pull request #175 from peastman/master

Fixed segfaults on some computers
Added AmoebaMultipoleForce::getInducedDipoles()
Merge pull request #176 from peastman/master

Added AmoebaMultipoleForce::getInducedDipoles()
Support gzip and bzip2 compression for StateDataReporter (based on filename
extension). Users were already able to pass gzip.GzipFile objects and
StateDataReporter would write compressed data. bz2.BZ2File objects also worked
after I removed the self._out.flush() calls.
Add sulphur and aluminium aliases.

Fix small bug in internal/pdbstructure.py.
Add the flush calls back to statedatareporter properly protected by try-except.
Merge pull request #178 from swails/master

Support gzip and bzip2 compression for StateDataReporter (based on filename extension) and other small fixes