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Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.


ABSTRACT: Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.

SUBMITTER: Arakawa T 

PROVIDER: S-EPMC3790736 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.

Arakawa Takamasa T   Kamiya Narutoshi N   Nakamura Haruki H   Fukuda Ikuo I  

PloS one 20131004 10


Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation metho  ...[more]

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