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Molecular Dynamics Simulation of Non-Simple Liquids

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Molecular Liquids: New Perspectives in Physics and Chemistry

Part of the book series: NATO ASI Series ((ASIC,volume 379))

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Abstract

In Molecular Dynamics Simulations the ensemble averages are obtained as time averages from the (classical mechanical) trajectories of the subsystems. For non-simple liquids, e.g. systems of complex organic molecules, this technique, in addition to extensive computer capacity also requires a very stable algorithm for solving the differential equation. The symplectic leap-frog algorithm and its extension the Nosé-Hoover-Leapfrog algorithm serve as a stable procedure for canonical-dynamical sampling.

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References

  1. Toxvaerd, S., (1991) ’Algorithms for canonical molecular dynamics simulations’, Molec.Phys. .72, 159–168.

    Article  CAS  Google Scholar 

  2. Verlet, L. , (1967) ’Computer Experiments on Classical Fluids’, Phys.Rev. 159, 98–103.

    Article  CAS  Google Scholar 

  3. Berendsen, H.G., and Van Gunsteren, W.F. (1986) ’Molecular Dynamics Simulations of Statistical Mechanical Systems’, in G. Ciccotti and W.G. Hoover (eds.), Proceedings of the International School of Physics ’Enrico Fermi’ Course XCVII, North-Holland pp 43–65.,

    Google Scholar 

  4. Miller, R.H., (1991), ’A horror story about integration methods’, J. Comput. Phys. 93, 469–476.

    Article  Google Scholar 

  5. Toxvaerd S., and Olsen O.H. (1990) ’Canonical Molecular Dynamics of Molecules with Internal Degrees of Freedom’, Ber. Bunsenges. Phys. Chem. 94, 274–278.

    Article  CAS  Google Scholar 

  6. Candy, J. and Rozmus, W. , (1991), ’A symplectic Integration algorithm for separable Hamiltonian functions’, J. Comput. Phys. 92, 230–256.

    Article  Google Scholar 

  7. Posch, H.A. and Hoover, W.G. (1989), ’Equilibrium and nonequilibrium Lyapunov spectra for dense fluids and solid’, Phys. Rev. A 39, 2175–2188.

    Article  Google Scholar 

  8. Nosé, S. (1984) ’A molecular dynamics method for simulations in the canonical ensemble’, Molec. Phys. 52, 255–268.

    Article  Google Scholar 

  9. Hoover, W.G. (1985) ’Canonical Dynamics. Equilibrium Phase-Space Distributions’, Phys. Rev. A31, 1695–1697.

    Google Scholar 

  10. See eg. Kusnezov D, Bulgac A. and Bauer, W. (1990) ’Canonical Ensembles from chaos I: classical systems’, Ann. Phys.( NY), 204. 155–162

    Article  CAS  Google Scholar 

  11. Cicotti, G. and Ryckardt, J.-P. (1981), ’On the derivation of the generalized Langevin equation for interacting Brownian particles’, J. stat. Phys. 26, 73–82.

    Article  Google Scholar 

  12. Bossis, G. , Quentrec, B., and Boon, J.-P. (1982), Brownian dynamics and the fluctuation-dissipation theorem’, Mol. Phys.45, 191–196.

    Article  CAS  Google Scholar 

  13. Toxvaerd, S. (1985), ’Solution of the generalized Langevin equation’, J. Chem. Phys. 82, 5658–5662,

    Article  CAS  Google Scholar 

  14. Toxvaerd, S. (1987) ’Solution of the generalized Langevin equation for a polymer in a solvent’, J.Chem. Phys. 86, 3667–3672.

    Article  CAS  Google Scholar 

  15. Brooks III, C.L. and Karplus, M. (1983), ’Deformable stochastic boundaries in molecular dynamics’, J. Chem. Phys. 79.6312–6325.

    Article  CAS  Google Scholar 

  16. Tuckerman, M.E., Martyna, G.J., and Berne, B.J. (1990) ’Molecular dynamics algorithm for condensed systems with multiple time scales’, J. Chem. Phys. 93, 1287–1291.

    Article  CAS  Google Scholar 

  17. Ryckaert, J.P., Cicotti, G., and Berendsen, H.J.C. (1977) ’Numrical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes’, J.Comput. Phys. 23, 327–341.

    Article  CAS  Google Scholar 

  18. Edberg, R., Evans, D.J., and Morriss, G.P. (1986),’Constrained molecular dynamics: Simulations of liquid alkanes with a new algorithm’, J. Chem. Phys. 84, 6933–6939.

    Article  CAS  Google Scholar 

  19. de Leeuw, S.W., Perram, J.W., and Petersen, H.G. (1990), ’Hamilton’s Equations for Constrained Dynamical Systems’, J. stat. Phys. 61, 1203–1221.

    Article  Google Scholar 

  20. Baranyai, A. and Evans, D.J. (1990), ’New algorithm for constrained molecular-dynamics simulation of liquid benzene and naphthalene’, Molec. Phys. 70, 53–63.

    Article  CAS  Google Scholar 

  21. Morriss, G.P. and Evans, D.J. (1991), ’A constrained algorithm for the computer simulation, of complex molecular liquids’, Computer Phys. Communications 62, 267–278.

    Article  CAS  Google Scholar 

  22. Ryckaert, J.P. and Bellemans, A. (1975), ’Molecular Dynamics of Liquid n-Butane near its Boiling Point’, Chem. Phys. Lett. 30, 123–125.

    Article  CAS  Google Scholar 

  23. Ryckaert, J.P. and Klein, M.L. (1986), ’Trans1ational and rotational disorder in solid n-alkanes: Constant temperature-constant pressure molecular dynamics calculations using infinitely long flexible chains’, J. Chem. Phys. 85, 1613– 1620.

    Article  CAS  Google Scholar 

  24. Toxværd, S. (1990), ’Molecular dynamics calculations of the equation of state of alkanes’, J. Chem. Phys. 93, 4290–4295.

    Article  Google Scholar 

  25. Lustig, R. and Steele, W.A. (1988), ’On the thermodynamics of liquid propane. A molecular dynamics study’, Molec. Phys. 65. 475–486.

    Article  CAS  Google Scholar 

  26. Padilla, P. and Toxvaerd, S. (1991), ’Second virial coefficient of n-alkanes’, Molec. Phys. (submitted).

    Google Scholar 

  27. Padilla, P. and Toxvaerd, S. (1991), ’ Self-diffusion in n- alkane fluid models’, J. Chem. Phys. 94, 5650–5654.

    Article  CAS  Google Scholar 

  28. Padilla, P. and Toxvaerd, S. (1991), ’Structure and dynanical behavior of fluid n-alkanes’, J. Chem. Phys. 95, 909–519.

    Article  Google Scholar 

  29. Bachl, F. and Lüdemann, H.-D. (1986), ’Pressure and Temperature Dependence of Self-Diffusion in Liquid Linear Hydrocarbons’, Z. Naturforsch 41a, 963–970.

    CAS  Google Scholar 

  30. Habenschuss, A. and Norten, A.H. (1990), ’X-ray diffraction study of some liquid alkanes’, J. Chem. Phys. 97, 5692–5699.

    Article  Google Scholar 

  31. Boreman, J.P., Cardini, G. and Klein, M.L. (1988), ’Characterization of Structural and Dynamical Behaviour in Monolayers of Long-Chain Molecules Using Molecular-Dynamics Calculations’, Phys. Rev. Lett. 60, 2152–2155.

    Article  Google Scholar 

  32. Moller, M.A., Tildesley, D.J. and Kim, K.S. (1991), ’Molecular Dynamics simulation of a Langmuir-Blodgett film’, J. Chem. Phys. 94, 8390–8401.

    Article  CAS  Google Scholar 

  33. Bishop, M. and Clarke, J. H.R. (1991), ’System size dependence and time convergence in molecular dynamics simulations of monolayer films’, J. Chem. Phys. 95, 540–543.

    Article  CAS  Google Scholar 

  34. Karaborni, S. and Toxvaerd, S. (1991), ’Molecular Dynamics Simulations of Langmuir Monolayers: A Study of Structure and Thermodynamics, J. Chem. Phys. (submitted).

    Google Scholar 

  35. Karaborni, S. and Toxvaerd, S. (1991), ’Computer simulations of amphiphilic molecules at the air-water interface’, Nature (submitted).

    Google Scholar 

  36. Ställberg-Stenhagen S., and Stenhagen, E. (1945), ’Phase Transitions in Condensed Monolayers of Normal Chain Carboxylic Acids’, Nature 156, 239–240.

    Article  Google Scholar 

  37. Lundquist, M. (1970), ’The Relation between Polymorphism in “Two-dimensional” Monolayers Films on Water’, Chem. Scr. 1, 5– 20).

    Google Scholar 

  38. Kenn, R.M., Böhm, C. , Bibo, A. Peterson, I.R., Möhwald, H. , Als-Nielsen J. , and Kjaer, K. (1991), ’Mesophases and Crystalline Phases in Fatty Acid Monolayers, J. Phys. Chem. 95. 2092–2097.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, H.C. Ørsted Institute, Dk-2100, Copenhagen Ø, Denmark

    Søren Toxvaerd

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  1. Søren Toxvaerd
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Editors and Affiliations

  1. Departamento de Química, Universidade de Coimbra, Coimbra, Portugal

    José J. C. Teixeira-Dias

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© 1992 Springer Science+Business Media Dordrecht

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Toxvaerd, S. (1992). Molecular Dynamics Simulation of Non-Simple Liquids. In: Teixeira-Dias, J.J.C. (eds) Molecular Liquids: New Perspectives in Physics and Chemistry. NATO ASI Series, vol 379. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-2832-2_10

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  • DOI: https://doi.org/10.1007/978-94-011-2832-2_10

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5258-0

  • Online ISBN: 978-94-011-2832-2

  • eBook Packages: Springer Book Archive

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