Build Nanostructures (Bottlebrush Polymers) for MD Simulations
In the last tutorial, generation of hard-soft nanomaterials was demonstrated. In many other cases, soft-soft assemble systems are also seen, for example, polymer grafted bottle-brush polymers (BBPs). Here, generation of backbone chains, side chains and eventually the assemble BBPs will be demonstrated.
General procedures
The procedures are the same as previous examples. The only difference is to assemble distinct pieces together, i.e., backbone polymer and side chain polymer. Here the PVA as the backbone chain, and PEO as side chains. The general steps (including subsequent MD simulations) are:
- generate the pdb file of PVA polymer (using SMILES) to generate a straight chain
- generate the pdb file of PEO polymer (using SMILES) to generate a straight chain
- calculate the grafting density and determine the grafting sites on the backbone chain
- transform (rotate and/or translate) the PEO to the grafting sides accordingly
- output the assembled structure in pdb format
- correct the generated pdb file as per Gromacs requirements
- define the residue/atom in specified force field
- convert pdb file into coordinate and topology files
- run MD simulations in Gromacs
The generated PVA30-g-PEO8 system (with a grafting density of 1) before and after equilibration is rendered as:
The generated PVA50-g-PEO15 system (with a grafting density of 1) before and after equilibration is rendered as:
With these systems, many interesting aspects can be studied. Stay Tuned!