Issue 45, 2009
From the journal:

Physical Chemistry Chemical Physics

The impact of monovalent ion force field model in nucleic acids simulations

Agnes Noy,a   Ignacio Soteras,b   F. Javier Luqueb  and  Modesto Orozco*cde  

* Corresponding authors

a Department of Physics and Astronomy, University of Sheffield, Sheffield, UK

b Departament de Fisicoquímica and Institut de Biomedicina. Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain

c Joint IRB-BSC program on Computational Biology, Institut de Recerca Biomèdica. Parc Científic de Barcelona. Josep Samitier 1-5., Barcelona 08028 and Barcelona Supercomputer Center., Jordi Girona 31. Edifici Torre Girona., Barcelona 08028, Spain
E-mail: modesto@mmb.pcb.ub.es

d Departament de Bioquímica. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain

e National Institute of Bioinformatics. Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain

Abstract

Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.

Graphical abstract: The impact of monovalent ion force field model in nucleic acids simulations

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Article information

DOI
https://doi.org/10.1039/B912067J
Article type
Paper
Submitted
19 Jun 2009
Accepted
28 Jul 2009
First published
18 Aug 2009

Phys. Chem. Chem. Phys., 2009,11, 10596-10607

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The impact of monovalent ion force field model in nucleic acids simulations

A. Noy, I. Soteras, F. Javier Luque and M. Orozco, Phys. Chem. Chem. Phys., 2009, 11, 10596 DOI: 10.1039/B912067J

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