1. Model Preparation: The first step involves selecting the system to be studied and preparing a computational model. This includes obtaining the structure of the molecule or enzyme, which can be sourced from databases like the Protein Data Bank (PDB).
2. Setting up the Simulation: Parameters such as the force field (e.g., AMBER, CHARMM) and the simulation environment (e.g., solvent type, temperature) are defined. The system is then equilibrated to ensure stability.
3. Running the Simulation: The actual simulation runs, typically involving solving Newtonâs equations of motion for all atoms in the system over a specified time period.
4. Analysis: Post-simulation, data is analyzed to extract meaningful insights. This can involve studying the trajectories, energy profiles, and interaction patterns.
