GitLab

Created API and reference implementation of restricting CustomNonbondedForce to selected interaction groups

Fixed some compilation errors

Get the version number from the CMake script

create a simtk.openmm.version module that contains the git revision

Speed optimization to GromacsTopFile

Eliminated a potential stack overflow when identifying molecules

Moved Python app layer tests into the main source tree

ForceField tries to figure out why no residue matched a template

Converted the routine for identifying molecules from a recursion to a loop.  This avoids stack overflows with very long linear molecules.

Cache the PTX files for compiled kernels

Fix segfault when positions are not 3 dimensional.

Lots of updates to documentation for new features in 5.2.

Added an argument to addHydrogens() for selecting which Platform to use for minimization. Also marked convertWater() as deprecated.

Added an argument to addHydrogens() for selecting which Platform to use for minimization.  Also marked convertWater() as deprecated.

Include process ID in temporary file names to avoid collisions

Updated to newer version of cl.hpp

Added SWM4-NDP water model

Changed order of arguments to produce a simpler API