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mosdef-hub
Flexible storage of chemical topology for molecular simulation
This PR starts adding support for periodic improper potentials as they were recently added to Hoomd version 4.5. I'm running into some issues, I figured I'd get the PR submitted...
Add support to write out the settles section for gromacs top file. Decision still need to be made about what would be considered the appropriate flag/signal/label to indicate that the...
This PR looks to improve the handling for converting a topology to a dataframe. This currently lives as a method for topology. It is now being moved to a convert_dataframe.py...
Once https://github.com/mosdef-hub/mbuild/pull/1180 passes I think we should do the same here; adding python 3.12 to the CI workflow, updating the `.yml` files to include python 3.12 and make sure the...
Current GROMACS writer didn't take into the case of system with non-element site. This leads to a wide range of errors that may not be obvious to user. The method...
Subclasses of `Connection` should have a function `measure()` that measures that bond/angle/dihedral. This will be good for sanity-checking your simulation. Things to consider: * How we want to implement (define...
Would be useful to check the charge of the topology or subtopologies.
Is there a way to join several topologies to make one big topology? An example use case would be if you have one molecule typed with a particular force field...
It seems there is an error with a path function in the `gmso.external.convert_foyer_xml_write_gmso_xml function`. However, it seems to do the foyer to gmso XML conversion properly. I attached a simple...
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Flexible storage of chemical topology for molecular simulation