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广义等温等压系综-分子动力学模拟全原子水的气液共存形貌

尹灵康 徐顺 Seongmin Jeong Yongseok Jho 王健君 周昕

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Citation:

广义等温等压系综-分子动力学模拟全原子水的气液共存形貌

尹灵康, 徐顺, Seongmin Jeong, Yongseok Jho, 王健君, 周昕

Vapor-liquid coexisting morphology of all-atom water model through generalized isothermal isobaric ensemble molecular dynamics simulation

Yin Ling-Kang, Xu Shun, Seongmin Jeong, Yongseok Jho, Wang Jian-Jun, Zhou Xin
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  • 探测相变过程中瞬时共存相的形貌等特征对理解其微观机制十分重要.本文应用广义等温等压系综-分子动力学模拟方法,研究全原子水模型的气液两相平衡及相变的中间过程.研究发现,此广义系综方法能够通过持续降温,连续地历经从气态、气液共存到液态的整个相变过程,通过持续升温历经其相反过程,而不会发生标准正则系综中的过饱和热滞现象.该方法不需要使用副本交换等增强抽样方法,因此可以用于较大体系的研究,多个独立的模拟即能获得整个气态液态区的平衡性质及共存相特征.本文还提出了计算气液共存界面面积的新方法,给出了水的气液共存界面形状随温度、压强的变化规律.结果表明,低压时水的气液共存界面因其较大的表面张力而接近球面,符合经典成核理论的描述,但随着压强升高接近其临界压强时,气态和液态的差别减小,界面的表面张力变小,界面形状变为无规则的枝杈结构,表现为二阶相变特征.
    Exploring the atom-scale details such as morphology of coexisting phase during phase transitions is very important for understanding their microscopic mechanism.While most theories,such as the classic nucleation theory,usually over-simplify the character of the critical nucleus,like the shape,structure,and most current experiment techniques are hardly to capture the instantaneous microscopic details,the atomistic molecular dynamics (MD) or Monte Carlo (MC) simulation provides a promise to detect the intermediate process of phase transitions.However,the standard canonicalensemble MD/MC simulation technique can not sufficiently sample the instantaneous (unstable in thermodynamics) coexistent phase.Therefore,the MC in the general canonical ensemble,such as general isothermal-volume ensemble (gNVT),combined with the enhanced sampling techniques,such as the replica exchange (RE) method,was presented to stabilize then to sufficiently sample the atomic conformations of the phase coexistence.Due to the limit of the RE, the RE-MC simulation on gNVT is usually applied in smaller systems.In this paper,we first extend the gNVT-based MC simulation to the MD in the generalized isothermal-isobaric ensemble (gNPT) and very simply implement it in the standard atomic MD soft packages without modifying the code,so that we can use these packages in MD simulation of realistic systems.Then we simulate the vapour-liquid phase transition of all-atomic water model.At least at not very low pressures,we find that the individual gNPT simulation is already enough to reach equilibrium in any region of the phase transition,not only in the normal liquid and vapour regions,but in the super-saturation regions,and even in the vapour-liquid coexistent regions.The obtained energy-temperature curve in the cooling gNPT well matches with that in the heating procedure without any hysteresis.It indicates that it is not necessary to use the RE technique in the gNPT,and the intermediate states during phase transitions in larger systems can be effectively simulated by a series of independent individual gNPT-MD simulations in the standard soft packages.We also propose a method to accurately determine the interface between the two phases in the coexistence,then provide a quantitative measurement about the interface tension and the morphology of the coexistent phase in the larger all-atomic water at various temperatures and pressures.The results show that the liquid droplet (or vapour bubble) at the low pressure is close to a sphere due to the larger interface tension,as expectation of the classic nucleation theory of the first-order phase phase transition,but becomes more and more irregular as the decrease of the interfacial tension as increasing the pressure to approach to the critical pressure,where the phase transition is the second order one.
      通信作者: 周昕, xzhou@ucas.ac.cn
    • 基金项目: 国家自然科学基金(批准号:11574310)资助的课题.
      Corresponding author: Zhou Xin, xzhou@ucas.ac.cn
    • Funds: Project supported by the National Natural Science Foundation of China (Grant No.11574310).
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    Toxvaerd S 2015 J. Chem. Phys. 143 154705

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    Debenedetti P G 2006 Nature 441 168

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    Myerson A S, Trout B L 2013 Science 341 855

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    Savage J R, Dinsmore A D 2009 Phys. Rev. Lett. 102 198302

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    Sleutel M, van Driessche A E 2014 Proc. Natl. Acad. Sci. 111 E546

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    de Yoreo J 2013 Nature Mater. 12 284

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    Yarom M, Marmur A 2015 Adv. Colloid Interface Sci. 222 743

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    Duöka M, Němec T, Hrubö J, Vinö V, Planková B 2015 EPJ Web Conf. 92 02013

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    Schenter G K, Kathmann S M, Garrett B C 1999 Phys. Rev. Lett. 82 3484

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    Reguera D, Reiss H 2004 Phys. Rev. Lett. 93 165701

    [17]

    Bhimalapuram P, Chakrabarty S, Bagchi B 2007 Phys. Rev. Lett. 98 206104

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    Rane K S, Murali S, Errington J R 2013 J. Chem. Theory Comput. 9 2552

    [19]

    Planková B, Vinö V, Hrubö J, Duöka M, Němec T, Celnö D 2015 EPJ Web Conf. 92 02071

    [20]

    McGrath M J, Kuo I F W, Ghogomu J N, Mundy C J, Siepmann J I 2011 J. Phys. Chem. B 105 11688

    [21]

    Malolepsza E, Kim J, Keyes T 2015 Phys. Rev. Lett. 114 170601

    [22]

    Kuo I F W, Mundy C J 2004 Science 303 658

    [23]

    Nagata Y, Usui K, Bonn M 2015 Phys. Rev. Lett. 115 236102

    [24]

    Zahn D 2004 Phys. Rev. Lett. 93 227801

    [25]

    Panagiotopoulos A Z 1987 Mol. Phys. 61 813

    [26]

    Mouöka F, Nezbeda I 2013 Fluid Phase Equilib. 360 472

    [27]

    Trejos V M, Gil-Villegas A, Martinez A 2013 J. Chem. Phys. 139 184505

    [28]

    Cho W J, Kim J, Lee J, Keyes T, Straub J E, Kim K S 2014 Phys. Rev. Lett. 112 157802

    [29]

    Kim J, Keyes T, Straub J E 2010 J. Chem. Phys. 132 224107

    [30]

    Maöolepsza E, Secor M, Keyes T 2015 J. Phys. Chem. B 119 13379

    [31]

    Lu Q, Kim J, Straub J E 2013 J. Chem. Phys. 138 104119

    [32]

    Xu S, Zhou X, Ouyang Z C 2012 Commun. Comput. Phys. 12 1293

    [33]

    Jeong S, Jho Y, Zhou X 2015 Sci. Rep. 5 15955

    [34]

    Gloor G J, Jackson G, Blas F J, de Miguel E 2005 J. Chem. Phys. 123 134703

    [35]

    Vega C, de Miguel E 2007 J. Chem. Phys. 126 154707

    [36]

    Kumar V S, Kumaran V 2005 J. Chem. Phys. 123 114501

    [37]

    Zhu H X, Thorpe S M, Windle A H 2001 Philos. Mag. A 81 2765

    [38]

    Oger L, Gervois A, Troadec J P, Rivier N 1996 Philos. Mag. B 74 177

    [39]

    Plimpton S 1995 J. Comput. Phys. 117 1

    [40]

    Abascal J L, Vega C 2005 J. Chem. Phys. 123 234505

    [41]

    Vega C, Abascal J L F, Nezbeda I 2006 J. Chem. Phys. 125 034503

    [42]

    Beckers J V L, Lowe C P, de Leeuw S W 1998 Mol. Simul. 20 369

    [43]

    Nosé S 1984 J. Chem. Phys. 81 511

    [44]

    Hoover W G 1985 Phys. Rev. A 31 1695

    [45]

    Alejandre J, Chapela G A 2010 J. Chem. Phys. 132 014701

  • [1]

    Erdemir D, Lee A Y 2009 Acc. Chem. Res. 42 621

    [2]

    Sleutel M, Lutsko J, van Driessche A E, Durán-Olivencia M A, Maes D 2014 Nat. Commun. 5 5598

    [3]

    Auer S, Frenkel D 2004 Annu. Rev. Phys. Chem. 55 333

    [4]

    Toxvaerd S 2015 J. Chem. Phys. 143 154705

    [5]

    Debenedetti P G 2006 Nature 441 168

    [6]

    Gasser U, Weeks E R, Schofield A, Pusey P N, Weitz D A 2001 Science 292 258

    [7]

    Yasuoka K, Matsumoto M 1998 J. Chem. Phys. 109 8451

    [8]

    Yasuoka K, Matsumoto M 1998 J. Chem. Phys. 109 8463

    [9]

    Myerson A S, Trout B L 2013 Science 341 855

    [10]

    Savage J R, Dinsmore A D 2009 Phys. Rev. Lett. 102 198302

    [11]

    Sleutel M, van Driessche A E 2014 Proc. Natl. Acad. Sci. 111 E546

    [12]

    de Yoreo J 2013 Nature Mater. 12 284

    [13]

    Yarom M, Marmur A 2015 Adv. Colloid Interface Sci. 222 743

    [14]

    Duöka M, Němec T, Hrubö J, Vinö V, Planková B 2015 EPJ Web Conf. 92 02013

    [15]

    Schenter G K, Kathmann S M, Garrett B C 1999 Phys. Rev. Lett. 82 3484

    [16]

    Reguera D, Reiss H 2004 Phys. Rev. Lett. 93 165701

    [17]

    Bhimalapuram P, Chakrabarty S, Bagchi B 2007 Phys. Rev. Lett. 98 206104

    [18]

    Rane K S, Murali S, Errington J R 2013 J. Chem. Theory Comput. 9 2552

    [19]

    Planková B, Vinö V, Hrubö J, Duöka M, Němec T, Celnö D 2015 EPJ Web Conf. 92 02071

    [20]

    McGrath M J, Kuo I F W, Ghogomu J N, Mundy C J, Siepmann J I 2011 J. Phys. Chem. B 105 11688

    [21]

    Malolepsza E, Kim J, Keyes T 2015 Phys. Rev. Lett. 114 170601

    [22]

    Kuo I F W, Mundy C J 2004 Science 303 658

    [23]

    Nagata Y, Usui K, Bonn M 2015 Phys. Rev. Lett. 115 236102

    [24]

    Zahn D 2004 Phys. Rev. Lett. 93 227801

    [25]

    Panagiotopoulos A Z 1987 Mol. Phys. 61 813

    [26]

    Mouöka F, Nezbeda I 2013 Fluid Phase Equilib. 360 472

    [27]

    Trejos V M, Gil-Villegas A, Martinez A 2013 J. Chem. Phys. 139 184505

    [28]

    Cho W J, Kim J, Lee J, Keyes T, Straub J E, Kim K S 2014 Phys. Rev. Lett. 112 157802

    [29]

    Kim J, Keyes T, Straub J E 2010 J. Chem. Phys. 132 224107

    [30]

    Maöolepsza E, Secor M, Keyes T 2015 J. Phys. Chem. B 119 13379

    [31]

    Lu Q, Kim J, Straub J E 2013 J. Chem. Phys. 138 104119

    [32]

    Xu S, Zhou X, Ouyang Z C 2012 Commun. Comput. Phys. 12 1293

    [33]

    Jeong S, Jho Y, Zhou X 2015 Sci. Rep. 5 15955

    [34]

    Gloor G J, Jackson G, Blas F J, de Miguel E 2005 J. Chem. Phys. 123 134703

    [35]

    Vega C, de Miguel E 2007 J. Chem. Phys. 126 154707

    [36]

    Kumar V S, Kumaran V 2005 J. Chem. Phys. 123 114501

    [37]

    Zhu H X, Thorpe S M, Windle A H 2001 Philos. Mag. A 81 2765

    [38]

    Oger L, Gervois A, Troadec J P, Rivier N 1996 Philos. Mag. B 74 177

    [39]

    Plimpton S 1995 J. Comput. Phys. 117 1

    [40]

    Abascal J L, Vega C 2005 J. Chem. Phys. 123 234505

    [41]

    Vega C, Abascal J L F, Nezbeda I 2006 J. Chem. Phys. 125 034503

    [42]

    Beckers J V L, Lowe C P, de Leeuw S W 1998 Mol. Simul. 20 369

    [43]

    Nosé S 1984 J. Chem. Phys. 81 511

    [44]

    Hoover W G 1985 Phys. Rev. A 31 1695

    [45]

    Alejandre J, Chapela G A 2010 J. Chem. Phys. 132 014701

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出版历程
  • 收稿日期:  2017-03-29
  • 修回日期:  2017-05-04
  • 刊出日期:  2017-07-05

广义等温等压系综-分子动力学模拟全原子水的气液共存形貌

  • 1. 中国科学院大学物理科学学院, 北京 100049;
  • 2. 中国科学院计算机网络信息中心, 北京 100190;
  • 3. Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea;
  • 4. 中国科学院化学研究所, 北京 100190
  • 通信作者: 周昕, xzhou@ucas.ac.cn
    基金项目: 国家自然科学基金(批准号:11574310)资助的课题.

摘要: 探测相变过程中瞬时共存相的形貌等特征对理解其微观机制十分重要.本文应用广义等温等压系综-分子动力学模拟方法,研究全原子水模型的气液两相平衡及相变的中间过程.研究发现,此广义系综方法能够通过持续降温,连续地历经从气态、气液共存到液态的整个相变过程,通过持续升温历经其相反过程,而不会发生标准正则系综中的过饱和热滞现象.该方法不需要使用副本交换等增强抽样方法,因此可以用于较大体系的研究,多个独立的模拟即能获得整个气态液态区的平衡性质及共存相特征.本文还提出了计算气液共存界面面积的新方法,给出了水的气液共存界面形状随温度、压强的变化规律.结果表明,低压时水的气液共存界面因其较大的表面张力而接近球面,符合经典成核理论的描述,但随着压强升高接近其临界压强时,气态和液态的差别减小,界面的表面张力变小,界面形状变为无规则的枝杈结构,表现为二阶相变特征.

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