The European Physical Journal Special Topics

, Volume 225, Issue 8–9, pp 1595–1607 | Cite as

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

  • J. Zavadlav
  • R. Podgornik
  • M.N. Melo
  • S.J. Marrink
  • M. Praprotnik
Open Access
Regular Article Hybrid and Adaptive Coarse Graining Methods
Part of the following topical collections:
  1. Modern Simulation Approaches in Soft Matter Science: From Fundamental Understanding to Industrial Applications

Abstract

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

Supplementary material

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Copyright information

© The Author(s) 2016

Open Access This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • J. Zavadlav
    • 1
    • 2
  • R. Podgornik
    • 2
    • 3
  • M.N. Melo
    • 4
  • S.J. Marrink
    • 4
  • M. Praprotnik
    • 1
    • 2
  1. 1.Department of Molecular ModelingNational Institute of ChemistryLjubljanaSlovenia
  2. 2.Department of PhysicsFaculty of Mathematics and Physics, University of LjubljanaSI-1000 LjubljanaSlovenia
  3. 3.Theoretical Physics Department, J. Stefan InstituteLjubljanaSlovenia
  4. 4.Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of GroningenAG GroningenThe Netherlands

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