Skip to main content
SpringerLink
Log in

Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

  • Regular Article
  • Hybrid and Adaptive Coarse Graining Methods
  • Published:
The European Physical Journal Special Topics Aims and scope Submit manuscript

Abstract

In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

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.

Institutional subscriptions

Similar content being viewed by others

References

  1. G. Grest, K. Kremer, Phys. Rev. A. 33, 3628 (1986)

    Article  ADS  Google Scholar 

  2. K. Kremer, G. Grest, I. Carmesin, Phys. Rev. Lett. 61, 566 (1988)

    Article  ADS  Google Scholar 

  3. L. Yelash, M. Müller, W. Paul, K. Binder, J. Chem. Theory Comput. 2, 588 (2006)

    Article  Google Scholar 

  4. T. Spyriouni, C. Tzoumanekas, D. Theodorou, F. Müller-Plathe, G. Milano, Macromolecules 40, 3876 (2007)

    Article  ADS  Google Scholar 

  5. J. McCammon, M. Karplus, Nature 268, 765 (1977)

    Article  ADS  Google Scholar 

  6. M. Karplus, J. McCammon, Nature 277, 578 (1979)

    Article  ADS  Google Scholar 

  7. P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti, M. Parrinello, J. Phys. Chem. B. 110, 3533 (2006)

    Article  Google Scholar 

  8. H. Lou, R.I. Cukier, J. Phys. Chem. B. 110, 12796 (2006)

    Article  Google Scholar 

  9. K. Arora, C.L. Brooks, Proc. Natl. Acad. Sci. USA 104, 18496 (2007)

    Article  ADS  Google Scholar 

  10. F. Pontiggia, A. Zen, C. Micheletti, Biophys. J. 95, 5901 (2008)

    Article  ADS  Google Scholar 

  11. M.M. Tirion, D. ben Avraham, J. Mol. Biol. 230, 186 (1993)

    Article  Google Scholar 

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

    Article  ADS  Google Scholar 

  13. I. Bahar, A.R. Atilgan, B. Erman, Folding and Design 2, 173 (1997)

    Article  Google Scholar 

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

    Article  Google Scholar 

  15. R. Potestio, F. Pontiggia, C. Micheletti, Biophys. J. 96, 4993 (2009)

    Article  ADS  Google Scholar 

  16. C. Globisch, V. Krishnamani, M. Deserno, C. Peter, PLoS. ONE 8, e60582, 04 (2013)

    Article  Google Scholar 

  17. K. Kremer, Comput. Simul. Soft Matter Sci. 53 (2000)

  18. K. Kremer, F. Müller-Plathe, MRS Bull. 26, 205 (2001)

    Article  Google Scholar 

  19. N.A. van der Vegt, C. Peter, K. Kremer, Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations (CRC Press - Taylor and Francis Group, 2009)

  20. C. Hijón, E. Vanden-Eijnden, R. Delgado-Buscalioni, P. Español, Farad. Discuss. 144, 301 (2010); discussion 323–45, 467–81 (2010)

    Article  ADS  Google Scholar 

  21. W. Noid, Systematic Methods for Structurally Consistent Coarse-Grained Models, 924 of Methods in Molecular Biology (Humana Press, 2013)

  22. W.G. Noid, J. Chem. Phys. 139, 090901 (2013)

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

  25. M. Praprotnik, L. Delle Site, K. Kremer, J. Chem. Phys. 126, 134902 (2007)

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

  27. S. Fritsch, C. Junghans, K. Kremer, J. Chem. Theo. Comput. 8, 398 (2012)

    Article  Google Scholar 

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

    Article  ADS  Google Scholar 

  29. 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 

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

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

  32. K. Kreis, D. Donadio, K. Kremer, R. Potestio, Europhys. Lett. 108, 30007 (2014)

    Article  Google Scholar 

  33. P. Español, R. Delgado-Buscalioni, R. Everaers, R. Potestio, D. Donadio, K. Kremer, J. Chem. Phys. 142, 064115 (2015)

    Article  ADS  Google Scholar 

  34. B.J. Lambeth, C. Junghans, K. Kremer, C. Clementi, L. Delle Site, J. Chem. Phys. 133, 221101 (2010)

    Article  ADS  Google Scholar 

  35. A.C. Fogarty, R. Potestio, K. Kremer, J. Chem. Phys. 142, 195101 (2015)

    Article  ADS  Google Scholar 

  36. P.P. Ewald, Ann. Phys. 64, 253 (1921)

    Article  Google Scholar 

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

    Article  Google Scholar 

  38. J.A. Barker, R.O. Watts, Mol. Phys. 26, 789 (1973)

    Article  ADS  Google Scholar 

  39. D. van der Spoel, P.J. van Maaren, H.J.C. Berendsen, J. Chem. Phys. 108, 10220 (1998)

    Article  ADS  Google Scholar 

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

    Article  ADS  Google Scholar 

  41. I. Fukuda, H. Nakamura, Biophys. Rev. 4, 161, (2012)

    Article  MathSciNet  Google Scholar 

  42. D. Wolf, P. Keblinski, S.R. Phillpot, J. Eggebrecht, J. Chem. Phys. 110, 8254 (1999)

    Article  ADS  Google Scholar 

  43. C.J. Fennell, J.D. Gezelter, J. Chem. Phys. 124, 23 (2006)

    Article  Google Scholar 

  44. M.A. Kastenholz, P.H. Hünenberger, J. Phys. Chem. B 108, 774 (2004)

    Article  Google Scholar 

  45. D.A.C. Beck, R.S. Armen, V. Daggett, Biochemistry 44, 609 (2005)

    Article  Google Scholar 

  46. R.D. Lins, U. Röthlisberger, J. Chem. Theo. Comput. 2, 246 (2006)

    Article  Google Scholar 

  47. S. Plimpton, J. Comput. Phys. 117, 1 (1995)

    Article  ADS  Google Scholar 

  48. R.W. Hockney, J.W. Eastwood, Computer simulation using particles (CRC Press, 1988)

  49. J. Kirkwood, J. Chem. Phys. 3, 300 (1935)

    Article  ADS  Google Scholar 

  50. M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1987)

  51. D. Van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, H.J.C. Berendsen, J. Comp. Chem. 26, 1701 (2005)

    Article  Google Scholar 

  52. D. Wolf, Phys. Rev. Lett. 68, 3315 (1992)

    Article  ADS  Google Scholar 

  53. S. Fritsch, R. Potestio, D. Donadio, K. Kremer, J. Chem. Theory Comput. 10, 816 (2014) PMID: 26580055

    Article  Google Scholar 

  54. F. Bresme, A. Lervik, D. Bedeaux, S. Kjelstrup, Phys. Rev. Lett. 101, 020602 (2008)

    Article  ADS  Google Scholar 

  55. J.R. Errington, P.G. Debenedetti, Nature 409, 318 (2001)

    Article  ADS  Google Scholar 

  56. J. Kohanoff, Comput. Mat. Sci. 2, 221 (1994)

    Article  Google Scholar 

  57. T. Youngs, “dlputils: Calculate properties from molecular dynamics trajectories”, (2016) https://www.projectaten.com/dlputils

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

    Article  Google Scholar 

  59. L.X. Dang, B.M. Pettitt, J. Phys. Chem. 91, 3349 (1987)

    Article  Google Scholar 

  60. Y. Wu, H.L. Tepper, G.A. Voth, J. Chem. Phys. 124, 2 (2006)

    Google Scholar 

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

    Article  ADS  Google Scholar 

  62. E. Duboué-Dijon, D. Laage, J. Phys. Chem. B, 119, 8406 (2015) PMID: 26054933

    Article  Google Scholar 

  63. C. Avendaño, A. Gil-Villegas, Mol. Phys. 104, 1475 (2006)

    Article  ADS  Google Scholar 

  64. T.G. Desai, J. Chem. Phys. 127 (2007)

  65. Y. Nagata, S. Mukamel, J. Amer. Chem. Soc. 132, 6434 (2010)

    Article  Google Scholar 

  66. E.E. Gdoutos, R. Agrawal, H.D. Espinosa, Inter. J. Numer. Meth. Eng. 84, 1541 (2010)

    Article  Google Scholar 

  67. W. Shi, E.J. Maginn, J. Phys. Chem. B 112, 2045 (2008)

    Article  Google Scholar 

  68. K. Kreis, A.C. Fogarty, K. Kremer, R. Potestio, Eur. Phys. J. Special Topics 224, 2289 (2015)

    Article  ADS  Google Scholar 

  69. S. Bellissima, M. Neumann, E. Guarini, U. Bafile, F. Barocchi, Phys. Rev. E 92, 042166, (2015)

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany

    M. Heidari, R. Cortes-Huerto, D. Donadio & R. Potestio

  2. Department of Chemistry, University of California Davis, One Shields Ave. Davis, CA, 95616, USA

    D. Donadio

Authors
  1. M. Heidari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Cortes-Huerto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. Donadio
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. Potestio
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. Potestio.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Heidari, M., Cortes-Huerto, R., Donadio, D. et al. Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations. Eur. Phys. J. Spec. Top. 225, 1505–1526 (2016). https://doi.org/10.1140/epjst/e2016-60151-6

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1140/epjst/e2016-60151-6

Search

Navigation