Zielinski François, Popelier Paul L A
Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain, UK.
J Mol Model. 2014 Jul;20(7):2256. doi: 10.1007/s00894-014-2256-y. Epub 2014 Jun 24.
The point-charge approximation, typically used by classical molecular mechanics force-fields, can be overcome by a multipolar expansion. For decades multipole moments were only used in the context of the rigid body approximation but recently it has become possible to combine multipolar electrostatics with molecular flexibility. The program DL_MULTI, which is derived from DL_POLY_2, includes efficient multipolar Ewald functionality up to the hexadecapole moment but the code is restricted to rigid bodies. The incorporation of flexibility into DL_MULTI would cause too large an impact on its architecture whereas the package DL_POLY_4 offers a more attractive and sustainable route to handle multipolar electrostatics. This package inherently handles molecular flexibility, which warrants sufficiently transferable atoms or atoms that are "knowledgeable" about their chemical environment (as made possible by quantum chemical topology and machine learning). DL_MULTI uses the spherical multipole formalism, which is mathematically more involved than the Cartesian one but which is more compact. DL_POLY_4 uses the computationally efficient method of smooth particle mesh Ewald (SPME) summation, which has also been parallellized by others. Therefore, combining the strengths of DL_POLY_4 and DL_MULTI poses the challenge of merging SPME with multipolar electrostatics by spherical multipole. In an effort to recast as clearly as possible the principles behind DL_MULTI, its key equations have been reformulated by the more streamlined route involving the algebra of complex numbers, and some of these equations' peculiarities clarified. This article explores theoretically the repercussions of the merging of SPME with spherical multipole electrostatics (as implemented in DL_MULTI). Difficulties in design and implementation of possible future code are discussed.
经典分子力学力场通常采用的点电荷近似可以通过多极展开来克服。几十年来,多极矩仅在刚体近似的背景下使用,但最近已能够将多极静电学与分子柔性相结合。源自DL_POLY_2的程序DL_MULTI包括高效的多极埃瓦尔德功能,最高可达十六极矩,但代码仅限于刚体。将柔性纳入DL_MULTI会对其架构造成太大影响,而DL_POLY_4软件包提供了一条更具吸引力且可持续的途径来处理多极静电学。该软件包本质上能处理分子柔性,这就需要足够可转移的原子或对其化学环境“了解”的原子(这可通过量子化学拓扑学和机器学习实现)。DL_MULTI使用球多极形式,其在数学上比笛卡尔形式更复杂,但更紧凑。DL_POLY_4使用计算效率高的光滑粒子网格埃瓦尔德(SPME)求和方法,其他人也已将其并行化。因此,结合DL_POLY_4和DL_MULTI的优势带来了通过球多极将SPME与多极静电学合并的挑战。为了尽可能清晰地重述DL_MULTI背后的原理,其关键方程已通过涉及复数代数的更简化途径重新表述,并阐明了其中一些方程的特性。本文从理论上探讨了SPME与球多极静电学合并(如在DL_MULTI中实现)的影响。讨论了未来可能代码在设计和实现中的困难。