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We need a general and robust way of creating an MDAnalysis trajectory object from MMSchema for [TrajToMdaComponent](https://github.com/MolSSI/mmic_mda/blob/master/mmic_mda/components/traj_component.py…
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ATM the [Molecule](https://github.com/MolSSI/MMElemental/blob/bdb389d6abd7b38dd22dda749af66adfa949b15e/mmelemental/models/molecule/mm_molecule.py#L45) model stores atomic information for a single fra…
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This is probably actually a problem with ParmEd, but I just wanted to record this somewhere. The [particular `alanine.pdb` file](https://github.com/MolSSI/mm_data/blob/main/mm_data/molecules/alanine.p…
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The purpose of this issue is to suggest building a "component" for auto_martini (dubbed `mmic_ffpa_autom`) that makes it part of the [MMIC](https://mm-portal.netlify.app/mmic) ecosystem [MolSSI](http:…
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Inconsistent hash found in model reconstruction when using the `mmic_parmed` molecule converter.
## Code snippet
```python
import mmelemental
mol = mmelemental.models.Molecule.from_file(some…
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Hi everyone, I was updating the component `mmic_optim_gmx` and I encountered a bug about the hash value in `Molecule` object. This bug is from `from_file()` function, which is an inherent function of …
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**Description**
Writing a [Molecule](https://github.com/MolSSI/MMElemental/blob/master/mmelemental/models/molecule/mm_mol.py#L54) object to a .gro file fails with [mmic_parmed](https://github.com/Mol…
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As discussed off-github, it would be great to get MDAnalysis and MMElemental talking.
I'm opening this issue to look into what needs to be addressed in order to implement such a converter.
The m…
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[`mm_molecule.Molecule.to_file()`](https://github.com/MolSSI/MMElemental/blob/master/mmelemental/models/molecule/mm_molecule.py) must be refactored and its internals moved to [`molwriter_component.Mol…