分子动力学是一套分子模拟方法，该方法主要是依靠计算机来模拟分子、原子体系的运动，是一种多体模拟方法。通过对分子、原子在一定时间内运动状态的模拟，从而以动态观点考察系统随时间演化的行为。通常，分子、原子的轨迹是通过数值求解牛顿运动方程得到，势能（或其对笛卡尔坐标的一阶偏导数，即力）通常可以由分子间相互作用势能函数、分子力学力场、从头算给出。对于考虑分子本身的量子效应的体系，往往采用波包近似处理或采用量子力学的费恩曼路径积分表述方式处理。 分子动力学也常常被采用作为研究复杂体系热力学性质的采样方法。以在由分子体系的不同状态构成的系综中抽取样本，从而计算体系的构型积分，并以构型积分的结果为基础进一步计算体系的热力学量和其他宏观性质。 分子动力学最早在20世纪50年代由物理学家提出，如今广泛应用与物理、化学、生物体系的理论研究中。

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, and is thus a type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamical evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are calculated using interatomic potentials or molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules.