Day 1.
Molecular Dynamics Simulation
Morning Session:
- Introduction to Molecular Dynamics (MD)
- What is MD and its importance in computational chemistry and biology?
- Popular force fields in computer simulations and their applications.
Afternoon Session:
- Hands-on demonstration of running a simple MD simulation by using Gromacs software.
- Preparing input files and system parameters.
- Solvation and ionization of the system.
- Trajectory Analysis
- Analysis of MD trajectories.
Day 1 Milestones:
- Understanding the fundamental principles of Molecular Dynamics simulations.
- Hands-on experience of running a basic MD simulation.
- Basic knowledge of trajectory analysis.