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mosdef-hub
Flexible storage of chemical topology for molecular simulation
Thought motivated by [foyer #360](https://github.com/mosdef-hub/foyer/issues/360). I think this seems like a sensible thing to do. Depending on the force field, and particularly in the case of custom built force fields,...
Currently, we use XML 1.0 with `lxml` in python. I stumbled upon a package called [`xmlschema`](https://github.com/sissaschool/xmlschema) which has a decent user base, that can provide a way for validation for...
From a discussion in the pull request referenced below, a lot of our main data structures allow all arguments to be optional. In this example, we can make a potential...
Depending on the force field, bonds and angles can sometimes be fixed. Currently, we are unable to define whether or not these connections are fixed in the Foyer XML. Since...
At this point, I think we can incorporate some form of visualization for a topology. I am opening this issue to discuss options for visualization, libraries we want to use...
I want to get the discussion started on this. For now I'm mostly referring to the virtual interaction sites supported by Gromacs (ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf) although I think some of these are...
In `gmso`, the core objects are somewhat free form, they have no rules in general. For example you could change any property of any object regardless of its existence in...
@rsdefever That's a good point. maybe instead of merging equivalent connections, we could make sure that the connection members are sorted when writing to file to make it easier to...
Add extra bookkeeping record for sites_addition, deletion etc... among others.
This is a part of discussions we had around performance. We should add these generators for providing more flexibility to the API.
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Flexible storage of chemical topology for molecular simulation