Opposite phenomenon to the flying ice cube in molecular ynamics simulations of flexible TIP3P water

doi:10.1007/s40436-013-0024-3

Advances in Manufacturing

Opposite phenomenon to the flying ice cube in molecular ynamics simulations of flexible TIP3P water

Liu-Ming Yan • Chao Sun • Hui-Ting Liu

Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, People’s Republic of China

收稿日期:2013-04-17 修回日期:2013-04-25 出版日期:2013-06-25 发布日期:2013-04-28
作者简介:e-mail: liuming.yan@shu.edu.cn

Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water

Liu-Ming Yan • Chao Sun • Hui-Ting Liu

Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, People’s Republic of China

Received:2013-04-17 Revised:2013-04-25 Online:2013-06-25 Published:2013-04-28
About author:e-mail: liuming.yan@shu.edu.cn

摘要/Abstract

摘要： An opposite phenomenon to the flying ice cube where kinetic energy is drained from the high frequency vibrational motion to the low frequency translational motion and rotational motion (Harvey et al., J Comput Chem 19:726–740, 1998) is reported in molecular dynamics simulations of the flexible TIP3P water. It is found that kinetic energy is drained from the low frequency translational motion and rotational motion to the high frequency vibrational motion of the flexible TIP3P water. In addition,the equipartition theorem is not applicable to the flexible TIP3P water, but applicable to the rigid TIP3P water.However, the Maxwell–Boltzmann velocity distribution is satisfied for cases even the equipartition theorem is not applicable.

关键词: Molecular dynamics, Equipartition theorem , Rigid TIP3P water , Flexible TIP3P water , Flying ice cube, Maxwell–Boltzmann distribution function

Abstract: An opposite phenomenon to the flying ice cube where kinetic energy is drained from the high frequency vibrational motion to the low frequency translational motion and rotational motion (Harvey et al., J Comput Chem 19:726–740, 1998) is reported in molecular dynamics simulations of the flexible TIP3P water. It is found that kinetic energy is drained from the low frequency translational motion and rotational motion to the high frequency vibrational motion of the flexible TIP3P water. In addition,the equipartition theorem is not applicable to the flexible TIP3P water, but applicable to the rigid TIP3P water.However, the Maxwell–Boltzmann velocity distribution is satisfied for cases even the equipartition theorem is not applicable.

Key words: Molecular dynamics, Equipartition theorem , Rigid TIP3P water , Flexible TIP3P water , Flying ice cube, Maxwell–Boltzmann distribution function

Liu-Ming Yan,hao Sun,Hui-Ting Liu. Opposite phenomenon to the flying ice cube in molecular ynamics simulations of flexible TIP3P water[J]. Advances in Manufacturing, doi: 10.1007/s40436-013-0024-3.

Liu-Ming Yan,hao Sun,Hui-Ting Liu. Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water[J]. Advances in Manufacturing, doi: 10.1007/s40436-013-0024-3.

参考文献

1. Chandrasekhar S (1939) An introduction to the study of stellar structure. University of Chicago Press, Chicago, pp 49–53

2. Tolman RC (1918) A general theory of energy partition with applications to quantum theory. Phys Rev 11(4):261–275

3. Mart?´nez S, Pennini F, Plastino A et al (2002) On the equipartition and virial theorems. Phys A 305(1–2):48–51

4. Plastino AR, Lima JAS (1999) Equipartition and virial theorems within general thermostatistical formalisms. Phys Lett A 260(1–2):46–54

5. Uline MJ, Siderius DW, Corti DS (2008) On the generalized equipartition theorem in molecular dynamics ensembles and the microcanonical thermodynamics of small systems. J Chem Phys 128(12):124301

6. Schnack J (1998) Molecular dynamics investigations on a quantum system in a thermostat. Phys A 259(1–2):49–58

7. Shirts RB, Burt SR, Johnson AM (2006) Periodic boundary condition induced breakdown of the equipartition principle and other kinetic effects of finite sample size in classical hard-sphere molecular dynamics simulation. J Chem Phys 125(16):164102

8. Shirts RB, Shirts MR (2002) Deviations from the Boltzmann distribution in small microcanonical quantum systems: two approximate one-particle energy distributions. J Chem Phys 117(12):5564–5575

9. Bakunin OG (2005) Correlation effects and nonlocal velocity distribution functions. Phys A 346(3–4):284–294

10. Keffer DJ, Baig C, Adhangale P et al (2008) A generalized Hamiltonian-based algorithm for rigorous equilibrium molecular dynamics simulation in the canonical ensemble. J Non-Newton Fluid Mech 152(1–3):129–139

11. Campisi M (2005) On the mechanical foundations of thermodynamics:the generalized Helmholtz theorem. Stud Hist Philos Sci Part B 36(2):275–290

12. Criado-Sancho M, Jou D, Casas-Va´zquez J (2006) Nonequilibrium kinetic temperatures in flowing gases. Phys Lett A 350(5–6):339–341

13. Allen MP, Tildesley DJ (1990) Computer simulation of liquids.Oxford University Press, Oxford

14. Frenkel D, Smit B (2002) Understanding molecular simulation:from algorithms to applications, 2nd edn. Academic Press, NewYork

15. Harvey SC, Tan RKZ, Cheatham TE III (1998) The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J Comput Chem 19(7):726–740

16. Mohazzabi P, Helvey SL, McCumber J (2002) Maxwellian distribution in non-classical regime. Phys A 316(1–4):314–322

17. Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water.J Chem Phys 79(2):926–935

18. Liew CC, Inomata H, Arai K (1998) Flexible molecular models for molecular dynamics study of near and supercritical water.Fluid Phase Equilib 144(1–2):287–298

19. Neria E, Fischer S, KarplusM(1996) Simulation of activation free energies in molecular systems. J Chem Phys 105(5):1902–1921

20. Yan L, Zhu S, Ji X et al (2007) Proton hopping in phosphoric acid solvated NAFION membrane: a molecular simulation study.J Phys Chem B 111(23):6357–6363

21. Guillot B (2002) A reappraisal of what we have learnt during three decades of computer simulations on water. J Mol Liq 101(1–3):219–260

22. Smith W, Leslie M, Forester TR (2003) Computer code DL_POLY_2.14. 2003: CCLRC. Daresbury Laboratory, Daresbury

23. Nose´ S (1984) A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys 52(2):255–268

24. Nose´ S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys 81(1):511–519

25. Hockney RW (1970) Potential calculation and some applications.Methods Comput Phys 9:136–211

26. Krynicki K, Green CD, Sawyer DW (1978) Pressure and temperature dependence of self-diffusion in water. Faraday Discuss Chem Soc 66:199–208

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Opposite phenomenon to the flying ice cube in molecular ynamics simulations of flexible TIP3P water

Opposite phenomenon to the flying ice cube in molecular dynamics simulations of flexible TIP3P water

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