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Computer simulation of particles with position-dependent mass

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Abstract

In the present work a dynamical system is investigated, in which the particles’ mass depends on their position in space. The first case study is that of a single point-like particle in one dimension, whose Hamiltonian is numerically integrated with a first-order, energy-conserving algorithm; subsequently, the model is extended to a Lennard-Jones fluid in three dimensions. The features of both setups are examined, and a simple, exact method is devised to obtain, from a system of particles with position-dependent mass, the same equilibrium observables that would be measured in a conventional simulation. The properties of these dynamical systems are explored, with possible applications in the development of efficient sampling strategies.

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References

  1. M.E. Tuckermann, Statistical Mechanics: Theory and Molecular Simulation (Oxford University Press, 2010)

  2. D. Frenkel, B. Smit, Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science) (Academic Press, 2001)

  3. S. Fritsch, R. Potestio, D. Donadio, K. Kremer, J. Chem. Theor. Comput. 10, 816 (2014)

    Article  Google Scholar 

  4. W.F. van Gunsteren, X. Daura, A.E. Mark, GROMOS Force Field (John Wiley and Sons, Ltd, 2002)

  5. C. Oostenbrink, T. Soares, N. Vegt, W. Gunsteren, Eur. Biophys. J. 34, 273 (2005)

    Article  Google Scholar 

  6. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, D.A. Case, J. Comput. Chem. 25, 1157 (2004)

    Article  Google Scholar 

  7. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins: Structure, Function Bioinformatics 65, 712 (2006)

    Article  Google Scholar 

  8. J.L.F. Abascal, C. Vega, J. Chem. Phys. 123, 234505 (2005)

    Article  ADS  Google Scholar 

  9. F. Paesani, W. Zhang, D.A. Case, T.E. Cheatham, G.A. Voth, J. Chem. Phys. 125, 4507 (2006)

    Article  ADS  Google Scholar 

  10. Y. Wu, H.L. Tepper, G.A. Voth, J. Chem. Phys. 124, 024503 (2006)

    Article  ADS  Google Scholar 

  11. G.S. Fanourgakis, S.S. Xantheas, J. Chem. Phys. 128, 074506 (2008)

    Article  ADS  Google Scholar 

  12. S. Leon, N. van der Vegt, L. Delle Site, K. Kremer, Macromolecules 38, 8078 (2005)

    Article  ADS  Google Scholar 

  13. B. Hess, S. Leon, N. van der Vegt, K. Kremer, Soft Matter 2, 409 (2006)

    Article  ADS  Google Scholar 

  14. M.M. Tirion, Phys. Rev. Lett. 77, 1905 (1996)

    Article  ADS  Google Scholar 

  15. C. Micheletti, P. Carloni, A. Maritan, Proteins 55, 635 (2004)

    Article  Google Scholar 

  16. C. Chennubhotla, A.J. Rader, L.W. Yang, I. Bahar, Phys. Biol. 2, 173 (2005)

    Article  ADS  Google Scholar 

  17. R. Car, M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)

    Article  ADS  Google Scholar 

  18. J. Cao, G.A. Voth, J. Chem. Phys. 100, 5106 (1994)

    Article  ADS  Google Scholar 

  19. J. Grossman, E. Schwegler, E. Draeger, F. Gygi, G. Galli, J. Chem. Phys. 120, 300 (2004)

    Article  ADS  Google Scholar 

  20. J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter, Comput. Phys. Commun. 167, 103 (2005)

    Article  ADS  Google Scholar 

  21. M. Tuckerman, B.J. Berne, G.J. Martyna, J. Chem. Phys. 97, 1990 (1992)

    Article  ADS  Google Scholar 

  22. D.D. Humphreys, R.A. Friesner, B.J. Berne, J. Phys. Chem. 98, 6885 (1994)

    Article  Google Scholar 

  23. A. Heyden, D.G. Truhlar, J. Chem. Theory Comput. 4, 217 (2008)

    Article  Google Scholar 

  24. J.H. Park, A. Heyden, Mol. Simul. 35, 962 (2009)

    Article  MATH  Google Scholar 

  25. M. Praprotnik, L. Delle Site, K. Kremer, J. Chem. Phys. 123, 224106 (2005)

    Article  ADS  Google Scholar 

  26. S. Fritsch, S. Poblete, C. Junghans, G. Ciccotti, L. Delle Site, K. Kremer, Phys. Rev. Lett. 108, 170602 (2012)

    Article  ADS  Google Scholar 

  27. R. Potestio, S. Fritsch, P. Español, R. Delgado-Buscalioni, K. Kremer, R. Everaers, D. Donadio, Phys. Rev. Lett. 110, 108301 (2013)

    Article  ADS  Google Scholar 

  28. R. Potestio, P. Español, R. Delgado-Buscalioni, R. Everaers, K. Kremer, D. Donadio, Phys. Rev. Lett. 111, 060601 (2013)

    Article  ADS  Google Scholar 

  29. H. Goldstein, Classical Mechanics, 2nd edn. (Addison-Wesley Publishing Company, 1980)

  30. L. Landau, E. Lifshitz, in Mechanics, 3rd edn. (Butterworth-Heinemann, 1976), Vol. 1

  31. W.R. Rudnicki, B. Lesyng, S.C. Harvey, Biopolymers 34, 383 (1994)

    Article  Google Scholar 

  32. J. Turner, P. Weiner, B. Robson, R. Venugopal, H. Schubele, R. Singh, J. Comput. Chem. 16, 1271 (1995)

    Article  Google Scholar 

  33. S. Nose, J. Chem. Phys. 81, 511 (1984)

    Article  ADS  Google Scholar 

  34. S. Nose, Molecular Phys. 52, 255 (1984)

    Article  ADS  Google Scholar 

  35. P. Lançon, G. Batrouni, L. Lobry, N. Ostrowsky, Europhys. Lett. 54, 28 (2001)

    Article  ADS  Google Scholar 

  36. P. Ilg, V. Mavrantzas, H.C. Öttinger, in Multiscale Modeling and Coarse Graining of Polymer Dynamics: Simulations Guided by Statistical Beyond-Equilibrium Thermodynamics (Wiley-VCH Verlag GmbH & Co. KGaA, 2010), pp. 343–383

  37. A.A. Louis, Faraday Discuss. 144, 323 (2010)

    Article  Google Scholar 

  38. C. Hijon, P. Espanol, E. Vanden-Eijnden, R. Delgado-Buscalioni, Faraday Discuss. 144, 301 (2010)

    Article  ADS  Google Scholar 

  39. P. Espanol, I. Zuniga, Phys. Chem. Chem. Phys. 13, 10538 (2011)

    Article  Google Scholar 

  40. D. Fritz, K. Koschke, V.A. Harmandaris, N.F.A. van der Vegt, K. Kremer, Phys. Chem. Chem. Phys. 13, 10412 (2011)

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128, Mainz, Germany

    Raffaello Potestio

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  1. Raffaello Potestio
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Potestio, R. Computer simulation of particles with position-dependent mass. Eur. Phys. J. B 87, 245 (2014). https://doi.org/10.1140/epjb/e2014-50314-y

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  • DOI: https://doi.org/10.1140/epjb/e2014-50314-y

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