Molecular Dynamics simulations and Trajectory analysis

This section focuses on setting up your MD experiment, processing, analysing and visualising outputs from molecular dynamics simulations’ trajectories.

Trainers: France Fraternali, Timir Weston, MariaLaura De Sciscio, Oriol Gracia I Carmona

Overview:

This practical session provides hands-on training with setting up MD experiments on various titin domains and variants.

Learning outcomes:

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

• List the steps to set up your own MD simulation for titin domains, in wild-type and variant conditions
• Mutate and Clean your structure in preparation for MD simulation
• Decide the appropriate conditions for an MD simulation including box sizes and simulation time
• Process, analyse and visualise trajectories

Materials

• Link to preparation for MD presentation slides
• MD practical files
• Trajectory processing, analysis and visualisation presentation slides