Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.
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Adaptive resolution simulation of oligonucleotides
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21 December 2016
Research Article|
December 15 2016
Adaptive resolution simulation of oligonucleotides
Paulo A. Netz;
Paulo A. Netz
1Departamento de Físico-Química, Instituto de Química,
Universidade Federal do Rio Grande do Sul
, Porto Alegre, RS 91501-970, Brazil
2
Max Planck Institut für Polymerforschung
, Ackermannweg 10, 55128 Mainz, Germany
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Raffaello Potestio
;
Raffaello Potestio
2
Max Planck Institut für Polymerforschung
, Ackermannweg 10, 55128 Mainz, Germany
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Kurt Kremer
Kurt Kremer
2
Max Planck Institut für Polymerforschung
, Ackermannweg 10, 55128 Mainz, Germany
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J. Chem. Phys. 145, 234101 (2016)
Article history
Received:
July 14 2016
Accepted:
November 22 2016
Citation
Paulo A. Netz, Raffaello Potestio, Kurt Kremer; Adaptive resolution simulation of oligonucleotides. J. Chem. Phys. 21 December 2016; 145 (23): 234101. https://doi.org/10.1063/1.4972014
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