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Issue 40, 2011
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A hybrid all-atom/coarse grain model for multiscale simulations of DNA

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Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.

Graphical abstract: A hybrid all-atom/coarse grain model for multiscale simulations of DNA

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Publication details

The article was received on 19 Apr 2011, accepted on 30 Aug 2011 and first published on 19 Sep 2011

Article type: Paper
DOI: 10.1039/C1CP21248F
Citation: Phys. Chem. Chem. Phys., 2011,13, 18134-18144

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    A hybrid all-atom/coarse grain model for multiscale simulations of DNA

    M. R. Machado, P. D. Dans and S. Pantano, Phys. Chem. Chem. Phys., 2011, 13, 18134
    DOI: 10.1039/C1CP21248F

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