Skip to main content
SpringerLink
Log in

Adaptive resolution simulation in equilibrium and beyond

  • Regular Article
  • A. Representation of Molecular Systems Across Scales
  • Published:
The European Physical Journal Special Topics Aims and scope Submit manuscript

Abstract

In this paper, we investigate the equilibrium statistical properties of both the force and potential interpolations of adaptive resolution simulation (AdResS) under the theoretical framework of grand-canonical like AdResS (GC-AdResS). The thermodynamic relations between the higher and lower resolutions are derived by considering the absence of fundamental conservation laws in mechanics for both branches of AdResS. In order to investigate the applicability of AdResS method in studying the properties beyond the equilibrium, we demonstrate the accuracy of AdResS in computing the dynamical properties in two numerical examples: The velocity auto-correlation of pure water and the conformational relaxation of alanine dipeptide dissolved in water. Theoretical and technical open questions of the AdResS method are discussed in the end of the paper.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

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

    Article  ADS  Google Scholar 

  2. M. Praprotnik, L. Delle Site, K. Kremer, Phys. Rev. E 73(6), 066701 (2006)

    Article  ADS  Google Scholar 

  3. M. Praprotnik, S. Matysiak, L. Delle Site, K. Kremer, C. Clementi, J. Phys: Condens. Matter 19, 292201 (2007)

    Google Scholar 

  4. M. Praprotnik, L. Delle Site, K. Kremer, Annu. Rev. Phys. Chem. 59, 545 (2008)

    Article  ADS  Google Scholar 

  5. A.B. Poma, L. Delle Site, Phys. Rev. Lett. 104(25), 250201 (2010)

    Article  ADS  Google Scholar 

  6. S. Poblete, M. Praprotnik, K. Kremer, L. Delle Site, J. Chem. Phys. 132, 114101 (2010)

    Article  ADS  Google Scholar 

  7. M. Praprotnik, S. Poblete, K. Kremer, J. Stat. Phys., 1 (2011)

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

    Article  ADS  Google Scholar 

  9. S. Bevc, C. Junghans, K. Kremer, M. Praprotnik, New J. Phys. 15, 105007 (2013)

    Article  ADS  Google Scholar 

  10. J. Zavadlav, M.M. Melo, S.J. Marrink, M. Praprotnik, J. Chem. Phys. 140(5), 054114 (2014)

    Article  ADS  Google Scholar 

  11. J. Zavadlav, M.N. Melo, A.V. Cunha, A.H. De Vries, S.J. Marrink, M. Praprotnik, J. Chem. Theor. Comput. 10(6), 2591 (2014)

    Article  Google Scholar 

  12. R. Delgado-Buscalioni, K. Kremer, M. Praprotnik, J. Chem. Phys. 131, 244107 (2009)

    Article  ADS  Google Scholar 

  13. B. Ensing, S.O. Nielsen, P.B. Moore, M.L. Klein, M. Parrinello, J. Chem. Theor. Comput. 3(3), 1100 (2007)

    Article  Google Scholar 

  14. D.M. Heyes, J. Chem. Phys. 132(6), 064504 (2010)

    Article  ADS  Google Scholar 

  15. Q. Shi, S. Izvekov, G.A. Voth, J. Phys. Chem. B 110(31), 15045 (2006)

    Article  Google Scholar 

  16. L. Shen, H. Hu, J. Chem. Theor. Comput. 10(6), 2528 (2014)

    Article  ADS  Google Scholar 

  17. S.O. Nielsen, P.B. Moore, B. Ensing, Phys. Rev. Lett. 105(23), 237802 (2010)

    Article  ADS  Google Scholar 

  18. M. Praprotnik, S. Poblete, L. Delle Site, K. Kremer, Phys. Rev. Lett. 107(9), 99801 (2011)

    Article  ADS  Google Scholar 

  19. L. Delle Site, Phys. Rev. E 76(4), 047701 (2007)

    Article  ADS  Google Scholar 

  20. H. Wang, C. Hartmann, C. Schütte, L. Delle Site, Phys. Rev. X 3(1), 011018 (2013)

    Google Scholar 

  21. R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, K. Kremer, R. Everaers, D. Donadio, Phys. Rev. Lett. 110(10), 108301 (2013)

    Article  ADS  Google Scholar 

  22. A. Agarwal, H. Wang, C. Schütte, L. Delle Site, J. Chem. Phys. 141, 034102 (2014)

    Article  ADS  Google Scholar 

  23. L. Delle Site, Entropy 16(1), 23 (2013)

    Article  Google Scholar 

  24. L. Onsager, J. Amer. Chem. Soc. 58(8), 1486 (1936)

    Article  Google Scholar 

  25. I.G. Tironi, R. Sperb, P.E. Smith, W.F. van Gunsteren, J. Chem. Phys. 102, 5451 (1995)

    Article  ADS  Google Scholar 

  26. D. Frenkel,B. Smit. Understanding molecular simulation (Academic Press, Inc. Orlando, FL, USA, 2001)

  27. H. Wang, J. Chem. Theor. Comput. 8(8), 2878 (2012)

    Article  ADS  Google Scholar 

  28. H.J.C. Berendsen, J.R. Grigera, T.P. Straatsma, J. Phys. Chem. 91(24), 6269 (1987)

    Article  Google Scholar 

  29. H. Wang, C. Junghans, K. Kremer, Eur. Phys. J. E: Soft Matter Biol. Phys. 28(2), 221 (2009)

    Article  Google Scholar 

  30. J.D. Weeks, D. Chandler, H.C. Andersen, J. Chem. Phys. 54(12), 5237 (1971)

    Article  ADS  Google Scholar 

  31. H. Wang, C. Schütte, G. Ciccotti, L. Delle Site, J. Chem. Theor. Comput. 10(4), 1376 (2014)

    Article  Google Scholar 

  32. M.S. Green, J. Chem. Phys. 22, 398 (1954)

    Article  MathSciNet  ADS  Google Scholar 

  33. R. Kubo, J. Phys. Soc. Jpn. 12(6), 570 (1957)

    Article  MathSciNet  ADS  Google Scholar 

  34. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, J. Chem. Phys. 79(2), 926 (1983)

    Article  ADS  Google Scholar 

  35. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, J.C. Smith, P.M. Kasson, D. van der Spoel, H.B. Lindahl E., Bioinformatics, 1 (2013)

  36. I. Fukuda, Y. Yonezawa, H. Nakamura, J. Chem. Phys. 134, 164107 (2011)

    Article  ADS  Google Scholar 

  37. I. Fukuda, J. Chem. Phys. 139, 174107 (2013)

    Article  ADS  Google Scholar 

  38. J. Apostolakis, P. Ferrara, A. Caflisch, J. Chem. Phys. 110(4), 2099 (1999)

    Article  ADS  Google Scholar 

  39. J.D. Chodera, N. Singhal, V.S. Pande, K.A. Dill, W.C. Swope, J. Chem. Phys. 126, 155101 (2007)

    Article  ADS  Google Scholar 

  40. J. Kaminskỳ, F. Jensen, J. Chem. Theor. Comput. 3(5), 1774 (2007)

    Article  Google Scholar 

  41. G. Feller, P. De Los Rios, A. Caflisch, F. Rao, Proc. Natl Acad. Sci. 104(6), 1817 (2007)

    Article  ADS  Google Scholar 

  42. N. Foloppe, A.D. MacKerell Jr., J. Comput. Chem. 21(2), 86 (2000)

    Article  Google Scholar 

  43. A.D. MacKerell, M. Feig, C.L. Brooks III, J. Comput. Chem. 25(11), 1400 (2004)

    Article  Google Scholar 

  44. J.-H. Prinz, B. Keller, F. Noé, Phys. Chem. Chem. Phys. 13(38), 16912 (2011)

    Article  Google Scholar 

  45. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J.D. Chodera, C. Schütte, F. Noé, J. Chem. Phys. 134, 174105 (2011)

    Article  ADS  Google Scholar 

  46. C. Schütte, F. Noé, J. Lu, M. Sarich, E. Vanden-Eijnden, J. Chem. Phys. 134, 204105 (2011)

    Article  ADS  Google Scholar 

  47. M. Sarich, F. Noé, C. Schütte, Multiscale Model. Simul. 8(4), 1154 (2010)

    Article  MathSciNet  Google Scholar 

  48. N. Djurdjevac, M. Sarich, C. Schütte, Multiscale Model. Simul. 10(1), 61 (2012)

    Article  MathSciNet  Google Scholar 

  49. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, T.R. Weikl, Proc. Natl. Acad. Sci. 106(45), 19011 (2009)

    Article  ADS  Google Scholar 

  50. K.J. Kohlhoff, D. Shukla, M. Lawrenz, G.R. Bowman, D.E. Konerding, D. Belov, R.B. Altman, V.S. Pande, Nat. Chem. 6(1), 15 (2014)

    Article  Google Scholar 

  51. M. Senne, B. Trendelkamp-Schroer, A.S.J.S. Mey, C. Schütte, F. Noé, J. Chem. Theor. Comput. 8(7), 2223 (2012)

    Article  Google Scholar 

  52. B.W. Kernighan, D.M. Ritchie, P. Ejeklint, The C programming language, Vol. 2 (Prentice-Hall Englewood Cliffs, 1988)

Download references

Author information

Authors and Affiliations

  1. CAEP Software Center for High Performance Numerical Simulation, Beijing, China

    H. Wang

  2. Zuse Institute Berlin (ZIB), Berlin, Germany

    H. Wang

  3. Institut für Mathematik, Freie Universität Berlin, Berlin, Germany

    A. Agarwal

Authors
  1. H. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Agarwal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to H. Wang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, H., Agarwal, A. Adaptive resolution simulation in equilibrium and beyond. Eur. Phys. J. Spec. Top. 224, 2269–2287 (2015). https://doi.org/10.1140/epjst/e2015-02411-2

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1140/epjst/e2015-02411-2

Keywords

Search

Navigation