Several key components are essential for conducting MD simulations:
Force Fields: Mathematical functions describing the potential energy of a system of particles. Initial Conditions: The starting positions and velocities of all atoms in the system. Time Integration Algorithms: Numerical methods to solve Newton's equations of motion over discrete time steps. Boundary Conditions: Rules defining the system's limits, such as periodic boundary conditions to simulate bulk properties. Simulation Software: Tools like GROMACS, LAMMPS, and AMBER that facilitate the execution and analysis of MD simulations.
