Basis of molecular dynamics simulations

Trainer: Alessandra Villa

Overview: These lectures will give you a broad overview of the theory behind molecular dynamics simulations, including force fields, thermostats and barostats, and boundary conditions.

Learning outcomes

By the end of this session you will be able to:

• Explain the theory and mathematics behind a molecular dynamics simulation, including approximations and sources of inaccuracies.
• Describe what a force field is and what its parameters are.
• Discuss the principles behind molecular models.
• Know how to pick an appropriate time-step.
• Discuss the theory and mathematics behind the thermodynamic principles in MD simulations.
• List the general workflow of a simulation and the GROMACS file types and naming system.

Materials

• Basis of molecular dynamics simulations – slides