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We need a way to initialize systems and run simulations that will help us model carbon fiber wetting. I have an mbuild function that will generate orthogonal sheets of graphene layers that we can use …
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This can be a thread where we can discuss some of the content we would want represented in this slideshow.
For now, I would break things down into five sections:
* Title Slide/Introduction
* mBu…
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I ran into the following error today when toying around with the example from our docs [here](https://mbuild.mosdef.org/en/stable/tutorials/tutorial_monolayer.html). The call that causes the error is …
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**Bug summary**
Atom order might not be definitive when loading from a SMILES string when using RDKit. Specifically, the index of the atoms when loading from a SMILES string with rdkit may changed …
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**Describe the behavior you would like added to mBuild**
All the user the option to specify the backend for saving files.
**Describe the solution you'd like**
Add a `backend` option to `Compound.…
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https://github.com/mosdef-hub/mbuild/blob/7da0c05b848e521d81aa8ad17194cc681a997389/mbuild/formats/lammpsdata.py#L1136
Even though the box has no tilt, this lines makes the modify kspace throw an erro…
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Currently the Cookiecutter is successfully building a directory with the correct file hierarchy. However I am unable to import this package due to an `ImportError` for the class within the `{{Cookiec…
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**Bug summary**
mbuild.Compound.energy_minimize() function fails if a GMSO formatted XML is used.
**Code to reproduce the behavior**
Make the mbuild.Compound.energy_minimize() function wo…
bc118 updated
2 years ago
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Current inputs can come from mbuild, parmed or openmm topologies + an xml file.
By default `Forcefield.apply()` yields a parmed structure but for users interested in running in OpenMM we can also e…
ctk3b updated
4 years ago
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**Is your feature request related to a problem? Please describe.**
Right now the user would need to write a custom function to read the final frame of a Cassandra trajectory.
**Describe the soluti…