This repository contains the material required for the workshop portion of the "Theoretical and Computational Chemistry: Modeling Methods in Chemical Engineering" course at the University of Chinese Academy of Sciences in June 2018.
There are five workshop sessions designed to onboard students that are new to molecular simulation to various simulation methods and engines. The MoSDeF toolkit is utilized as the workhorse for constructing and atom-typing molecular systems.
An overview of the MoSDeF toolkit, focusing primarily on mBuild. This session will also introduce users to Jupyter notebooks. There are four notebooks associated with this session:
- Introduction to Jupyter notebooks
- Introduction to MoSDeF
- Building simple systems with mBuild
- mBuild/Foyer/MD workflow example
An introduction to molecular dynamics using a simple Lennard-Jones system. This session will introduce students to the basics of a molecular dynamics simulation script. The HOOMD engine will be used in this session.
An introduction to atomistic molecular dynamics simulation. The GROMACS simulation engine will be used to simulate systems of bulk liquids.
An introduction to Monte Carlo simulation. Python-wrapped C++ code is used to perform Monte Carlo simulations of a simple Lennard-Jones system.
Advanced molecular dynamics simulations. Specifically, this session will focus on using the SLLOD equations of motion to perform a non-equilibrium molecular dynamics simulation of bulk alkanes.