This tutorial will build a composite model with a hydrophilic cellulose nanofibril enclosed by a hydrophobic polypropylene matrix. The protocol will define in separate steps how to build the structure models for the individual components and later to use the simulated annealing method to combine the components and generate the composite model.
The protocol will require familiarity with using the versatile MD simulations package GROMACS. It also requires basic knowledge about electronic structure methods to understand generating AMBER14 force field parameters. In addition, it will require structure visualization software such as PyMol or VMD.
It is recommended to first go through the tutorials of building models for cellulose nanofibril in a water box and a polypropylene box. If you have already completed those or prefer to skip that part then download the geometries for cellulose nanofibril with 10 cellobiose units and for the (poly)propylene chain composed of 10 monomers.