Coarse Graining Generation

[jbieri]

Cannot get coarse graining using GRiTS to work in the coarse-grain.ipynb. Produced mol2 and xml using the SMILES string shown in the attached image but it "cannot be found in the molecule."

A single frame GSD of this molecule can be produced using the single molecule sim in poly_min_working_example.ipynb as set up here

[erjank]

I don't know how you can expect someone to test this out without them having access to the gsd file. Either provide instructions for how to generate it, or provide a minimal trajectory (1 frame) for debugging.

[erjank]

For this molecule, we have 121 atoms in the repeat unit, so slicing through positions[18::121] would give you sulfurs down the backbone, please calculate the persistence length for this subset before fighting with coarse-graining