基于分子动力学的常用力场、算法及结果分析(2)

2019-05-17 18:34

手段。泰森多边形指数常用的形式表示,其中ni代表着Voronoi多面体具有的i边形数[38]。

第一近邻的配位数也是一种传统的分析微观结构的方式,此概念首先由阿尔弗雷德·维尔纳提出,原来更多地用于化学结构的表征,是配位化学的基础。在微观结构的表征中,配位数是用来描述中心原子第一壳层内原子的平均数目,反映的是中心原子与其它原子的结合能力和配位关系,描述的是体系中粒子排列的紧密程度,配位数越大,粒子排列越紧密。一般来说配位数是通过对径向分布函数的第一峰进行积分来得到。对于Voronoi指数分析而言,由于泰森多边形的算法就是计算中心原子与配位原子之间的连线平分面,因此,通过对Voronoi指数的累加,也能得到中心原子的配位数。对于晶体结构,通过配位数可以判断出晶体的结构;对于液态的非晶态结构,配位数可以作为一个发生结构转变的敏感参量,为结构转变的判断提供依据。例如,对于液体中发生的液?液相变现象,众多研究[39]都将配位数的变化作为判断的依据之一。

4展望

如果分子体系足够小,我们又有足够的耐心,即便只使用为数不多的处理器,完成微秒甚至是毫秒级时间尺度的模拟已不成问题,几年前就已经实现。然而,只有大规模并行架构,特别是千兆级运算速度的超级计算机的出现, 我们才得以处理数百万个原子组成的分子体系。但现阶段,毫秒级时间尺度或者百万原子空间尺度的分子模拟仍然构成技术上的巨大挑战,这恰恰又昭示着一个新时代的来临。随着第一台千兆级浮点运算速度的超级计算机投入使用,科学家已经开始期待着亿亿级计算机的到来并开始考虑这种新型架构将能够处理的分子体系的种类。

假使在未来的几十年,分子动力学的发展仍然紧跟摩尔定律所预测的计算机发展趋势,van Gunsteren[40]乐观地预测,未来20年内,我们将可以在纳秒级时间尺度上模拟一个完整的细菌,如大肠杆菌,大约20年后,可以模拟一个完整的哺乳动物细胞。这些基于目前硬件性能和软件发展水平所作出的推测固然很振奋人心,但我们应该清楚地认识到横亘在模拟时间尺度和空间尺度之间的鸿沟依然难以逾越。在未来的计算机模拟中,利用直接无偏分子动力学模拟研究生物大体系,有可能提供时间相关和动力学相关信息。而实现这一目标,我们仍然还有很长的路要走。

参考文献:

[1] Alder B J, Wainwright T E. Phase transition for a hard sphere system[J]. The Journal of chemical physics, 1957, 27(5): 1208.

[2] 赵继成. 材料基因组计划简介[J]. 自然杂志, 2014, 36(2): 89-104.

[3] Brooks B R, Bruccoleri R E, Olafson B D, et al. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations[J]. Journal of computational chemistry, 1983, 4(2): 187-217.

[4] Weiner S J, Kollman P A, Case D A, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins[J]. Journal of the American Chemical Society, 1984, 106(3): 765-784.

[5] Izvekov S, Voth G A. A multiscale coarse-graining method for biomolecular systems[J]. The Journal of Physical Chemistry B, 2005, 109(7): 2469-2473.

[6] Marrink S J, Risselada H J, Yefimov S, et al. The MARTINI force field: coarse grained model for biomolecular simulations[J]. The Journal of Physical Chemistry B, 2007, 111(27): 7812-7824. [7] Klein M L, Shinoda W. Large-scale molecular dynamics simulations of self-assembling systems[J]. Science, 2008, 321(5890): 798-800.

[8] Allinger N L, Yuh Y H, Lii J H. J Am Chem Soc 111: 8551;(b) Lii JH[J]. Allinger NL (1989) J Am Chem Soc, 1989, 111: 8566.

[9] Allinger N L, Chen K, Lii J H. An improved force field (MM4) for saturated hydrocarbons[J]. Journal of computational chemistry, 1996, 17(5‐6): 642-668.

[10] Sun H. COMPASS: an ab initio force-field optimized for condensed-phase applications

overview with details on alkane and benzene compounds[J]. The Journal of Physical Chemistry B, 1998, 102(38): 7338-7364. [11] Rappé A K, Casewit C J, Colwell K S, et al. UFF, a full periodic table force field for

molecular mechanics and molecular dynamics simulations[J]. Journal of the American chemical society, 1992, 114(25): 10024-10035. [12] Nosé S. A molecular dynamics method for simulations in the canonical ensemble[J]. Molecular physics, 1984, 52(2): 255-268.

[13] Hoover W G. Canonical dynamics: equilibrium phase-space distributions[J]. Physical review A, 1985, 31(3): 1695.

[14] Andersen H C. Molecular dynamics simulations at constant pressure and/or temperature[J]. The Journal of chemical physics, 1980, 72(4): 2384-2393.

[15] Darden T, York D, Pedersen L. Particle mesh Ewald: An N? log (N) method for Ewald sums in large systems[J]. The Journal of chemical physics, 1993, 98(12): 10089-10092. [16] Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics[J]. The Journal of chemical physics, 1992, 97(3): 1990-2001.

[17] Izaguirre J A, Reich S, Skeel R D. Longer time steps for molecular dynamics[J]. The Journal of chemical physics, 1999, 110(20): 9853-9864.

[18] Miyamoto S, Kollman P A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models[J]. Journal of computational chemistry, 1992, 13(8): 952-962. [19] Brown D, Clarke J H R, Okuda M, et al. A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines[J]. Computer Physics Communications, 1993, 74(1): 67-80. [20] Chipot C, ángyán J G. Continuing challenges in the parametrization of intermolecular force fields. Towards an accurate description of electrostatic and induction terms[J]. New journal of chemistry, 2005, 29(3): 411-420.

[21] Sagui C, Pedersen L G, Darden T A. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations[J]. The Journal of chemical physics, 2004, 120(1): 73-87.

[22] Nanoscience: Nanobiotechnology and nanobiology[M]. Springer Science & Business Media, 2009.

[23] Plimpton S. Fast parallel algorithms for short-range molecular dynamics[J]. Journal of computational physics, 1995, 117(1): 1-19.

[24] Hess B, Kutzner C, Van Der Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation[J]. Journal of chemical theory and computation, 2008, 4(3): 435-447.

[25] Stone J E, Phillips J C, Freddolino P L, et al. Accelerating molecular modeling applications with graphics processors[J]. Journal of computational chemistry, 2007, 28(16): 2618-2640. [26] Anderson J A, Lorenz C D, Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units[J]. Journal of Computational Physics, 2008, 227(10): 5342-5359.

[27] March N H, Tosi M P, March N H. Introduction to liquid state physics[M]. Singapore: World Scientific, 2002.

[28] Abraham F F. An isothermal–isobaric computer simulation of the supercooled‐liquid/glass transition region: Is the short‐range order in the amorphous solid fcc?[J]. The journal of chemical physics, 1980, 72(1): 359-365.

[29] Cheng Y Q, Ma E. Atomic-level structure and structure–property relationship in metallic glasses[J]. Progress in Materials Science, 2011, 56(4): 379-473.

[30] Qi L, Dong L F, Zhang S L, et al. Glass formation and local structure evolution in rapidly cooled Pd Ni alloy melt under high pressure[J]. Physics Letters A, 2008, 372(5): 708-711.

[31] Kim T H, Kelton K F. Structural study of supercooled liquid transition metals[J]. The Journal of chemical physics, 2007, 126(5): 054513.

[32] Laio A, VandeVondele J, Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations[J]. The Journal of chemical physics, 2002, 116(16): 6941-6947.

[33] 孙民华. 液态物理概论[M]. 科学出版社, 2013.

[34] March N H, Tosi M P, March N H. Introduction to liquid state physics[M]. Singapore: World Scientific, 2002.

[35]Qi L, Dong L F, Zhang S L, et al. Glass formation and local structure evolution in rapidly cooled Pd 55 Ni 45 alloy melt: Molecular dynamics simulation[J]. Computational Materials Science, 2008, 42(4): 713-716.

[36] Honeycutt J D, Andersen H C. Molecular dynamics study of melting and freezing of small Lennard-Jones clusters[J]. Journal of Physical Chemistry, 1987, 91(19): 4950-4963.

[37] Liu C S, Zhu Z G, Xia J, et al. Molecular dynamics simulation of the local inherent structure of liquid silicon at different temperatures[J]. Physical Review B, 1999, 60(5): 3194.

[38] Shi-Liang Z, Xin-Yu Z, Lin-Min W, et al. Voronoi Structural Evolution of Bulk Silicon upon Melting[J]. Chinese Physics Letters, 2011, 28(6): 067104.

[39] Zhang S, Wang L M, Zhang X, et al. Polymorphism in glassy silicon: Inherited from liquid-liquid phase transition in supercooled liquid[J]. Scientific reports, 2015, 5.

[40] Van Gunsteren W F, Bakowies D, Baron R, et al. Biomolecular modeling: goals, problems, perspectives[J]. Angewandte Chemie International Edition, 2006, 45(25): 4064-4092.


基于分子动力学的常用力场、算法及结果分析(2).doc 将本文的Word文档下载到电脑 下载失败或者文档不完整,请联系客服人员解决!

下一篇:英语写作

相关阅读
本类排行
× 注册会员免费下载(下载后可以自由复制和排版)

马上注册会员

注:下载文档有可能“只有目录或者内容不全”等情况,请下载之前注意辨别,如果您已付费且无法下载或内容有问题,请联系我们协助你处理。
微信: QQ: