List of covered topics:
- Introduction to force fields and molecular dynamics.
- Overview of AMBER and AmberTools and its programs.
- Introduction to setting up and running simulations.
- Visualizing AMBER simulations.
- Overview of AMBER Force Fields / Solvent Models etc.
- Introduction to implicit solvent and binding energy calculations.
- Protein folding and advanced analysis.
- Designing good simulation projects.
- Dealing with non-standard residues.
- What to do if there is no crystal structure.
- Statistical mechanics for free energy calculations.
- QM/MM coupled potential simulations.
- Advanced sampling methods.
- Lipid bilayer simulations.
- GPU accelerated molecular dynamics simulations.