Into to GRiTS¶

import mbuild as mb
import numpy as np

from grits import backmap
from grits import CG_Compound

Coarse-graining¶

A CG_Compound is created using an mbuild.Compound and a dictionary of the form {"bead name": "bead SMARTS"}.

SMILES/SMARTS strings are ways of specifying chemical information in a string format. GRiTS uses openbabel for SMARTS matching and RDKit for loading SMILES representations.

The CG_Compound class is built on the mbuild.Compound class (more about mBuild) but has some extra feautures which make it convenient for coarse grain structures.

First we’ll load a 3-hexylthiophene polymer (P3HT) into an mbuild.Compound and define a color dictionary. (The color definitions are unnecessary but helpful for distinguishing the coarse-grained beads during visualization.)

p3ht = mb.load("../grits/tests/assets/P3HT_16.mol2")

p3ht_colors = {"_B": "blue", "_S": "orange"}

In the example below, the cg_beads dictionary specifies a thiophene ring to be mapped to a "_B" bead (B for backbone!) with the string "c1sccc1" and three alkyl carbons to be mapped to an "_S" bead (S for sidechain!) with the string "CCC".

And that’s all you need to create a CG_Compound! All the information for bonding and backmapping is inferred during initialization.

cg_beads = {"_B": "c1sccc1", "_S": "CCC"}

cg_p3ht = CG_Compound(p3ht, cg_beads)

cg_p3ht.visualize(color_scheme=p3ht_colors, show_atomistic=True).show()
cg_p3ht.visualize(color_scheme=p3ht_colors).show()

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Backmapping¶

Finally, after using a CG_compound model for a simulation, we may want to retrieve the atomistic structure. For this we can use the backmap function. A CG_Compound keeps track of the bonding and anchors during initialization and uses these to recreate the atomistic positions and bonds.

fine_grained = backmap(cg_p3ht)
fine_grained.visualize().show()

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol