RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
J Chem Phys. 2012 Aug 7;137(5):054314. doi: 10.1063/1.4739789.
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we treated. We discussed the origin of this difference between the two schemes and the dependence of this fact on the physical system. The use of the zero damping-factor will enhance the efficiency of practical computations, since the complementary error function is not employed. In addition, utilizing the zero damping-factor provides freedom from the parameter choice, which is not trivial in the zero-charge scheme, and eliminates the error function term, which corresponds to the time-consuming Fourier part under the periodic boundary conditions.
零偶极子求和方法被扩展到一般分子体系,并应用于各向同性水体系的分子动力学模拟。在我们之前的论文[I. Fukuda、Y. Yonezawa 和 H. Nakamura,J. Chem. Phys. 134, 164107(2011)]中,为了评估经典粒子系统的静电能,我们提出了零偶极子求和方法,该方法从概念上防止了简单截止截断人为产生的非零电荷和非零偶极子状态。在这里,我们考虑将该方案应用于分子体系,以及一般截止截断方案的一些基本方面。引入了一个在方案中协调成键相互作用和静电相互作用的思想,我们开发了一种特定的算法。与之前的研究一样,所得能量公式表示为简单的对相互作用函数和和,使得易于应用于高性能计算。通过与艾瓦尔德方法生成的静电能进行比较,数值研究了基于原子的截断的零偶极子求和方法计算的静电能的准确性。我们在 TIP3P 各向同性水体系中获得了截断长度大于 13 Å 时小于 0.01%的静电能误差,与传统截断方法相比,误差很小。在 MD 模拟中的静态特性和稳定性也令人满意。此外,测量了介电常数和距离依赖的 Kirkwood 因子,并证实了它们与粒子网格艾瓦尔德方法计算的介电常数和距离依赖的 Kirkwood 因子的一致性,尽管这种一致性不容易通过截断方法获得。我们发现,在实际截断距离范围内,零阻尼因子给出了最佳结果。实际上,与零电荷方案相比,在我们处理的分子体系中,零电荷和零偶极子方案中的阻尼效应不敏感。我们讨论了这两种方案之间差异的原因以及该事实对物理系统的依赖性。使用零阻尼因子将提高实际计算的效率,因为不使用互补误差函数。此外,使用零阻尼因子提供了自由选择参数的自由,这在零电荷方案中并非微不足道,并且消除了对应于周期性边界条件下耗时的傅里叶部分的误差函数项。