Update Session 1 (MoSDeF tutorials)

[summeraz]

Session 1 will be introductory tutorials to the use of MoSDeF. My plan is to have a primer on what Jupyter notebooks are and how to use them followed by two Jupyter notebooks on MoSDeF for the students to work through (I think it will be best if everything is filled in and we just walk through together):

• Intro_to_Jupyter.ipynb

  • Introductory lesson on what Jupyter notebooks are and how to use them (might be able to even take something from the Jupyter website)

• Intro_to_MoSDeF.ipynb

  • Introduction to MoSDeF from the point of view of a user that already has mBuild Compound classes and Foyer Forcefields developed
  • Having the students create a variety of diverse Compounds (linear alkanes, alkane box, surface-bound monolayer, tethered nanosphere, etc.) where we use the same class (that we import and show the docstring of) to create several different Compound instances with different chemistry.

• Building_Compounds.ipynb

  • Walk through building some Compounds using mBuild
  • Loading from a PDB file, adding Ports, stitching Ports together, functionalizing the chains, creating a box of alkanes
  • Saving the box of alkanes to a LAMMPS file, passing a simple Foyer forcefield (with just the atomtypes for C(H2), C(H3), and H)
  • Cat-ing the Foyer forcefield and the LAMMPS data file