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在各向异性可极化分子力学中,使用直至四极矩的通用短程穿透校正来对固相微萃取多极静电进行可扩展改进。

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

作者信息

Narth Christophe, Lagardère Louis, Polack Étienne, Gresh Nohad, Wang Qiantao, Bell David R, Rackers Joshua A, Ponder Jay W, Ren Pengyu Y, Piquemal Jean-Philip

机构信息

UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France.

UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France.

出版信息

J Comput Chem. 2016 Feb 15;37(5):494-506. doi: 10.1002/jcc.24257.

Abstract

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.

摘要

我们提出了一种将用于分布式多极子的光滑粒子网格埃瓦尔德(SPME)方法与短程电荷穿透校正进行通用耦合的方法,该校正用于修改电荷-电荷、电荷-偶极和电荷-四极能量。与从头算值相比,这种方法显著改善了静电作用,并且已经根据对称适应微扰理论参考数据进行了校准。我们测试了各种中性分子二聚体,并给出了单价和二价阳离子与水配体形成的配合物的结果。在TINKER-HP软件中实现AMOEBA和SIBFA可极化力场的背景下,讨论了校正的可转移性。在讨论多极分布的选择时,得出了关于未来经穿透校正的可极化力场的结论,强调了获得平衡且具有物理意义的分布矩时非虚假程序的必要性。最后,讨论了短程校正的SPME方法的可扩展性和并行性,表明阻尼函数对于周期性边界条件下复杂生物或生物无机系统的分子动力学模拟在计算上是可行且准确的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/726d/4730919/a9afc92a258b/nihms-737679-f0001.jpg

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