标题： 分子动力学模拟中具有刚性约束的局部温度测量 显示英文标题

标题： Local temperature measurement in molecular dynamics simulations with rigid constraints

摘要： 在模拟中对分子进行约束（如保持键长和/或角度恒定）会减少它们的自由度（DoF），这进而会影响这些模拟中的温度计算。 当测量局部温度时，例如 从子体积中的一组原子或从一个 笛卡尔方向的速度中测量，如果局部 DoF 计算不正确，结果可能会看起来不物理地违反动能的均分定理。 在这里，我们确定如何从任意笛卡尔分量动能正确计算局部温度，通过自洽地评估受这些约束的原子的 DoF。 该方法在各种测试系统上进行了验证，包括受温度梯度影响的系统和被墙壁限制的系统。 还表明，该方法可以作为检测由数值积分近似性质或不足的平衡时间导致的动能均分破坏的敏感测试。 作为实际演示，我们展示了即使在常用的 2 fs 时间步长下，由刚性键连接的 C 和 H 原子之间的动能均分也可能被破坏，并且这种均分破坏似乎能有用地区分构型过热。 显示英文摘要

摘要： Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g. from a set of atoms in a subvolume or from velocities in one Cartesian direction, the result can appear to unphysically violate equipartition of the kinetic energy if the local DoF are not correctly calculated. Here we determine how to correctly calculate local temperatures from arbitrary Cartesian component kinetic energies, accounting for general geometric constraints, by self-consistently evaluating the DoF of atoms subjected to those constraints. The method is validated on a variety of test systems, including systems subject to a temperature gradient and those confined between walls. It is also shown to provide a sensitive test for the breakdown of kinetic energy equipartition caused by the approximate nature of numerical integration or insufficient equilibration times. As a practical demonstration, we show that kinetic energy equipartition between C and H atoms connected by rigid bonds can be violated even at the commonly-used time step of 2 fs, and that this equipartition violation appears to usefully indicate configurational overheating.