MolekulardynamikMethoden

Molecular dynamics (MD) is a computational method used to model the physical movements of atoms and molecules over time. In MD, the particles interact via predefined force fields or potentials, and their trajectories are obtained by numerically integrating Newton's equations of motion. The resulting data provide insights into structural, thermodynamic, and dynamical properties of systems at the atomic scale.

Classical MD uses empirical or semi-empirical force fields to describe bonded and nonbonded interactions. Ab initio MD computes forces on the fly from quantum mechanical calculations, typically for small systems or where electronic effects are essential. Coarse-grained MD reduces resolution to accelerate sampling for large systems.

Simulations are performed in defined thermodynamic ensembles, such as NVE (constant energy), NVT (constant volume and temperature), and NPT (constant pressure and temperature). Temperature and pressure are maintained with thermostats (Nosé–Hoover, Langevin) and barostats (Parrinello-Rahman). Boundary conditions are usually periodic to mimic bulk behavior. The common time step for all-atom MD is on the order of 1 femtosecond, sometimes constrained to 2 fs or larger with bond constraints.

MD is widely used to study biomolecules (proteins, nucleic acids), materials, polymers, and liquids; it aids in understanding folding, diffusion, phase behavior, and reaction mechanisms. Limitations include the timescale gap between simulations and many real processes, accuracy of force fields, and finite-size effects. Advances in algorithms, parallel computing, and multiscale approaches continue to expand MD's reach. Popular software packages include GROMACS, AMBER, NAMD, and LAMMPS.