GitLab

Fixes to GromacsTopFile with different combining rules

Updated description of unit test that was added.

I’m not sure how to trigger the unit testing suite, but this code
should test the changes I’ve made.

This was changed to help debug my development.  I have now returned it
to the original behavior.

This should fix CI build errors in parent repository.

The old _is_gro_coord function inexplicably used split() even though
gro files fixed field (nb: the parsing was still done correctly).  Now
it uses fixed field substrings.

I have made things more technically correct: GROMACS processes pairs
and exclusions separately.  Also added proper support for fudgeLJ term.
Also added improved gro file parsing (technically it’s a fixed-field
format but this works too).

These lines were missed previously

This is the initial commit of my work in getting OpenMM GROMACS support
improved to the point where SMOG SBM simulations run out-of-the-box.
Further commits will be code cleanup.

Fixed test failure on Windows

Allow docs to build in Sphinx 1.3.1 and 1.5.1

Fixed bugs in multipoles with ZOnly axis type

Add script to build on my Jenkins machine

Let tests run up to 2 hours and have a 5 minute timeout for individual tests.

Can append to DCD files

And protect against possible spaces in directories

Fixed travis badge

Fixed error adding triclinic solvent boxes

Fixed failing tests

Eliminated RealOpenMM