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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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OpenMM, Amber, and Charmm #105

Open kyleabeauchamp opened 10 years ago

kyleabeauchamp commented 10 years ago

I wanted to point out a few things:

  1. OpenMM has a python Topology object that looks fairly similar to your Molecule object, which might be helpful for interconversion
  2. OpenMM has python-based amber and charmm readers (https://github.com/SimTk/openmm/tree/master/wrappers/python/simtk/openmm/app)
  3. (1) and (2) might provide a path to convert from amber, charmm, and OpenMM to any of the InterMol formats
mrshirts commented 10 years ago

Hi, Kyle-

Thanks for the input. A lot of the stuff in InterMol has been underdevelopment for quite a while (I think before most of the OpenMM converters except for the amber->openMM converter). Perhaps a 'Molecule' to 'Topology' converter would make sense.

We had iterated around with Peter Eastman a while back to try to find a way to link things together, but weren't able to really come to an agreement. This might be a prime time to start connecting things together again to reduce overlap.

We are planning on doing an alpha release early next week (just need to fix a few bugs with unit testing).

OpenMM has python-based amber and charmm readers

Clearly, there is a lot of stuff that would be useable here. When we release alpha, that would be a great time to reach out to various people (You, Jason Swails, Robert McGibbon etc). and figure out the best path forward to have both good OpenMM functionality and stand-alone tools that others can use.

kyleabeauchamp commented 10 years ago

Sounds good, I'm watching this repo (albeit not very carefully), so I'm somewhat aware of what's going on here.

mrshirts commented 10 years ago

Thanks for keeping up up to date!

mrshirts commented 10 years ago

Let's keep it open for now until contacts have been made.