The process of performing an MD simulation involves several steps:
System Preparation: Define the system, including the type and number of particles, and assign initial positions and velocities. Choice of Force Field: Select an appropriate force field to model the interactions between particles. Equilibration: Allow the system to reach a stable state by running a preliminary simulation to equilibrate temperature and pressure. Production Run: Perform the actual simulation, collecting data on particle positions, velocities, and other properties over time. Analysis: Analyze the simulation data to extract meaningful information and validate the results against experimental data if available.
