Pechlaner Maria, Dorta Andreas P, Lin Zhixiong, Rusu Victor H, van Gunsteren Wilfred F
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland.
XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Shenzhen, China.
J Comput Chem. 2021 Mar 5;42(6):418-434. doi: 10.1002/jcc.26466. Epub 2020 Dec 22.
An algorithm to apply bond-angle constraints in molecular dynamics simulations of macromolecules or molecular liquids is presented. It uses Cartesian coordinates and determines the Lagrange multipliers required for maintaining the constraints iteratively. It constitutes an alternative to the use of only distance constraints (DCs) between particles to maintain a particular geometry. DCs are unsuitable to maintain particular, for example, linear or flat, geometries of molecules. The proposed algorithm can easily handle bond-length, bond-angle, and dihedral-angle constraints simultaneously, as when calculating a potential of mean force along a dihedral-angle degree of freedom.
本文提出了一种在大分子或分子液体的分子动力学模拟中应用键角约束的算法。它使用笛卡尔坐标，并迭代地确定维持约束所需的拉格朗日乘子。它构成了一种替代方法，用于仅使用粒子间距离约束（DC）来维持特定几何形状。DC不适用于维持分子的特定几何形状，例如线性或平面几何形状。所提出的算法可以轻松地同时处理键长、键角和二面角约束，就像沿着二面角自由度计算平均力势时一样。
