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mosdef-hub
Flexible storage of chemical topology for molecular simulation
While converting from `parmed`, it might be nice to include extra attributes for gmso.AtomType object using a forcefield reference. Key things we are looking for are: 1. smarts definition 2....
A summary of the question or discussion topic. Since we are adding mixing rules to the foyer XML files, do we also want to add fixed bonds and angles variable/info...
I may have missed this if it already exists. Do we need to limit the equations/variable name or do we have a good method of comparing the LJ/Mie/Exp6, electrostatic, bond,...
We have refactored mbuild's box code contributed by @justinGilmer to a separate Python package (available [here](https://github.com/mosdef-hub/molbox)). It might be nice to extend the current Box implementation by wrapping the functionality...
While working on #552, I noticed that if we have a suite of systems that could cover most use cases ([see foyer example](https://github.com/mosdef-hub/foyer/tree/master/foyer/opls_validation)), it might be helpful to run all...
RDKit has a bunch of functionality that would be useful here, in particular paths to supporting some cheminformatics-heavy [file formats](http://rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html). In particular, SDF files a pretty information-rich in ways that...
Our group has many custom force fields for individual molecules that have been developed over the years. We would like to use `gmso` to store and use these force fields...
Some potentials are the same but can be expressed in different functional forms. E.g., a harmonic bond can be expressed as `V(r) = 0.5*k*(r-req)**2` or `V(r) = k*(r-req)**2`. Another example...
(Somewhat abstract) idea: Add unit test(s) to make sure that new features don't negatively affect the performance of GMSO. I'm not exactly sure what this looks like, but something along...
According to [the gromacs 2018 documentation](http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html#gro), a gro file can contain multiple frames of a trajectory. Currently in our `read_gro` logic, linked below; we do not appear to check for...
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Flexible storage of chemical topology for molecular simulation