分子力学Molecular mechanics

总势能 E = E_键伸缩 + E_键角弯曲 + E_二面角扭转 + E_范德华 + E_静电。键伸缩和键角弯曲通常用谐振势 k(r − r₀)²；扭转项用余弦级数；范德华作用用伦纳德-琼斯 12-6 势；静电作用用库仑定律和原子部分电荷。参数通过拟合实验数据和高精度量子化学计算获得。常见力场有 MM2/MM3（有机小分子）、AMBER 和 CHARMM（生物大分子）、OPLS 和 GAFF（药物分子）、UFF（通用）。

Total energy E = E_stretch + E_bend + E_torsion + E_vdW + E_electrostatic. Stretching and bending are usually harmonic, k(r − r₀)²; torsions use cosine series; van der Waals interactions use the Lennard-Jones 12–6 potential; electrostatics use Coulomb's law with partial atomic charges. Parameters are fitted to experimental data and high-level quantum calculations. Common force fields include MM2/MM3 for small organic molecules, AMBER and CHARMM for biomolecules, OPLS and GAFF for drug-like molecules, and UFF as a general field.

1946 年韦斯特海默和梅耶分别用力场计算位阻效应和联苯的旋转能垒。1960 年代起艾林格（MM2，1977）、拉夫森和沃谢尔发展了系统的分子力学方法和程序。2013 年卡普拉斯、莱维特和沃谢尔因“为复杂化学体系发展多尺度模型”（QM/MM 方法）获诺贝尔化学奖。

In 1946 Westheimer and Mayer, and others, used force fields to compute steric effects and the rotation barrier of biphenyls. From the 1960s Allinger (MM2, 1977), Lifson and Warshel developed systematic molecular-mechanics methods and programs. In 2013 Karplus, Levitt and Warshel received the Nobel Prize in Chemistry 'for the development of multiscale models for complex chemical systems', the QM/MM approach.

分子力学用于构象搜索、能量最小化、蛋白质结构优化、药物分子对接和分子动力学模拟。它不能描述化学键的断裂与生成（除非用反应力场 ReaxFF）、电子激发和极化效应。QM/MM 方法把反应中心用量子力学处理、其余部分用分子力学处理，适合研究酶催化反应。

Molecular mechanics is used for conformational searching, energy minimisation, protein structure refinement, docking of drug molecules and molecular dynamics. It cannot describe bond breaking and making (except with reactive force fields such as ReaxFF), electronic excitation or polarisation. QM/MM methods treat the reacting centre quantum-mechanically and the rest with molecular mechanics, suiting enzyme reactions.