Skills
- Working with biological systems: structure, protein functional dynamics, macromolecular interactions
- Evaluating molecular interactions with force fields:
- Bonded interactions
- Non-bonded interactions
- Cross terms
- Polarizable and reactive force fields
- Computing with molecular mechanics:
- Solvation: implicit/explicit solvation, water models
- Potential energy surface:
- Energy minimization: steepest-descent, conjugate gradient, Newton-Raphson
- Molecular dynamics
- Monte-Carlo simulations
- Extracting properties with statistical mechanics:
- Normal Mode Analysis
- Binding affinity:
Tools
Amber16, CHARMM, Wordom, PLANTS, VMD
Context
Lectures and practicals:
- "Molecular Simulations" by Rachel Schurhammer
- "Biostructure and Modeling" by Marco Cecchini and Roland Stote