Finegraining united atom to all-atom

[jennyfothergill]

Fine-graining is not implemented for system sized morphologies. It would be a good proof of concept to show that we can take a UA trajectory, add hydrogens, and run the relaxation workflow Matty described in Fig 8 of http://dx.doi.org/10.1080/08927022.2017.1296958

We could use a similar logic to the new add_hydrogens kwarg to CG_System.

[chrisjonesBSU]

I just thought about this while helping Marjan with something. Does GRiTS and smiles string matching work on united atom trajectories?

[JimmyRushing]

Is this helpful? This finegrains xml.

https://bitbucket.org/cmelab/morphct/src/master/morphct/code/fine_grainer.py

[jennyfothergill]

Grits can add hydrogens to a trajectory for coarse-graining https://grits.readthedocs.io/en/latest/grits.html#grits.coarsegrain.CG_Compound
but it's not implemented very well for fine graining purposes yet.

Does GRiTS and smiles string matching work on united atom trajectories?

yes, just use the add_hydrogens kwarg