Planta Piloto de Ingeniería Química, PLAPIQUI, Universidad Nacional del Sur, Camino La Carrindanga Km 7-CC: 717, Bahía Blanca, Argentina.
Chemical Engineering Department, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil.
J Chem Phys. 2017 Sep 28;147(12):124104. doi: 10.1063/1.5003636.
Sets of atoms collectively behaving as rigid bodies are often used in molecular dynamics to model entire molecules or parts thereof. This is a coarse-graining strategy that eliminates degrees of freedom and supposedly admits larger time steps without abandoning the atomistic character of a model. In this paper, we rely on a particular factorization of the rotation matrix to simplify the mechanical formulation of systems containing rigid bodies. We then propose a new derivation for the exact solution of torque-free rotations, which are employed as part of a symplectic numerical integration scheme for rigid-body dynamics. We also review methods for calculating pressure in systems of rigid bodies with pairwise-additive potentials and periodic boundary conditions. Finally, simulations of liquid phases, with special focus on water, are employed to analyze the numerical aspects of the proposed methodology. Our results show that energy drift is avoided for time step sizes up to 5 fs, but only if a proper smoothing is applied to the interatomic potentials. Despite this, the effects of discretization errors are relevant, even for smaller time steps. These errors induce, for instance, a systematic failure of the expected equipartition of kinetic energy between translational and rotational degrees of freedom.
在分子动力学中，通常使用一组原子作为刚体来模拟整个分子或其部分。这是一种粗粒化策略，它消除了自由度，并允许在不放弃模型原子特性的情况下采用更大的时间步长。在本文中，我们依赖于旋转矩阵的特定分解来简化包含刚体的系统的力学公式。然后，我们提出了一种新的无扭矩旋转的精确解的推导方法，该方法被用作刚体动力学辛数值积分方案的一部分。我们还回顾了具有对加势能和周期性边界条件的刚体系统中压力的计算方法。最后，使用液体相的模拟，特别关注水，来分析所提出方法的数值方面。我们的结果表明，能量漂移可以避免高达 5fs 的时间步长，但前提是对原子间势进行适当的平滑处理。尽管如此，离散化误差的影响仍然是相关的，即使对于较小的时间步长也是如此。这些误差会导致，例如，平移和旋转自由度之间的期望动能分配的系统失效。
