Aaron Virshup

Thanks for this suggestion, @paleozogt . I definitely understand the motivation here, although I unfortunately don't believe such functionality could be easily supported with the way the program's written right...

Thanks for your comments and issues, @epcim! I agree that would definitely be great to have methods for additional parameterization within the docker-makefile. For my personal use cases, docker build-args...

In progress at /DEVELOPMENT.md TODO: - more Conda, less PyEnv - dev version synchronization with nbmolviz - Encourage py3 as the target, then backport as necessary to py2

@dane1122 - a couple issues I'm running into: - [x] The LAMMPS integrator throws an error when using the base LAMMPS potential model, e.g.: ```python import moldesign as mdt from...

Code is looking good! I'll play with it a bit when I get into the office. In the meantime, could you check on these two test failures? [test_lammps_shake_constrain_hbonds](https://travis-ci.org/Autodesk/molecular-design-toolkit/builds/220779318#L2124) [test_minimization_reduces_energy](https://travis-ci.org/Autodesk/molecular-design-toolkit/builds/220779318#L1993)

@dane1122 ~looks like we're getting a NameError at `lammps_model.py:147`~ Oh right, this because LAMMPS isn't installed on Travis, and we're not building the docker container yet (future PR). So never...

Implemented `moldesign._tests.test_topology_preserved_in_serialization`, which for now only has SDF bonds working correctly ...

@obrien951 - hey Joseph; do you have the docker engine installed on your machine? I suspect that's what the problem is. If true, then MDT needs to emit a better...

Hey @obrien951 and @loriab - Huge apologies for not getting to this yet. @ktbolt and I are working through getting a working version of MDT 0.8 out into the wild,...

@obrien951 - I'm FINALLY taking a look at this. And it looks good! I'm making a few changes to update it for the most recent version of the code (mostly...